diff --git a/cmd/status.go b/cmd/status.go
index ed59619..3b7098d 100644
--- a/cmd/status.go
+++ b/cmd/status.go
@@ -297,6 +297,8 @@ func detectSyncIssues(gitClient git.GitClient, stackBranches []stack.StackBranch
 		fmt.Printf("Checking %d branch(es) for sync issues...\n", len(stackBranches))
 	}
 
+	baseBranch := stack.GetBaseBranch(gitClient)
+
 	// Check each stack branch for sync issues
 	for i, branch := range stackBranches {
 		progress(fmt.Sprintf("Checking branch %d/%d (%s)...", i+1, len(stackBranches), branch.Name))
@@ -327,8 +329,23 @@ func detectSyncIssues(gitClient git.GitClient, stackBranches []stack.StackBranch
 			} else if verbose {
 				fmt.Printf("  ✓ PR base matches configured parent\n")
 			}
-		} else if verbose {
-			fmt.Printf("  No PR found for this branch\n")
+		} else {
+			// No PR found — check if branch appears merged via git history
+			if verbose {
+				fmt.Printf("  No PR found, checking git history for merge...\n")
+			}
+			merged, err := gitClient.IsAncestor(branch.Name, "origin/"+baseBranch)
+			if err == nil && merged {
+				if verbose {
+					fmt.Printf("  ✓ Branch appears merged into %s via git history\n", baseBranch)
+				}
+				issues = append(issues, fmt.Sprintf("  - Branch '%s' appears merged into %s (run '%s' to clean up)", ui.Branch(branch.Name), ui.Branch(baseBranch), ui.Command("stack prune")))
+				continue // Skip other checks for merged branches
+			} else if err != nil && verbose {
+				fmt.Printf("  ⚠ Could not check if branch is ancestor: %v\n", err)
+			} else if verbose {
+				fmt.Printf("  No PR found for this branch\n")
+			}
 		}
 
 		// Check if branch is behind its parent (needs rebase) - always check this regardless of PR
diff --git a/cmd/status_test.go b/cmd/status_test.go
index bde6075..21a1620 100644
--- a/cmd/status_test.go
+++ b/cmd/status_test.go
@@ -118,6 +118,7 @@ func TestDetectSyncIssues(t *testing.T) {
 			},
 			prCache: make(map[string]*github.PRInfo),
 			setupMocks: func(mockGit *testutil.MockGitClient) {
+				mockGit.On("IsAncestor", "feature-a", "origin/main").Return(false, nil)
 				mockGit.On("IsCommitsBehind", "feature-a", "main").Return(true, nil)
 				mockGit.On("RemoteBranchExists", "feature-a").Return(false)
 			},
@@ -130,11 +131,23 @@ func TestDetectSyncIssues(t *testing.T) {
 			},
 			prCache: make(map[string]*github.PRInfo),
 			setupMocks: func(mockGit *testutil.MockGitClient) {
+				mockGit.On("IsAncestor", "feature-a", "origin/main").Return(false, nil)
 				mockGit.On("IsCommitsBehind", "feature-a", "main").Return(false, nil)
 				mockGit.On("RemoteBranchExists", "feature-a").Return(false)
 			},
 			expectedIssues: 0,
 		},
+		{
+			name: "branch merged via git history (no PR)",
+			stackBranches: []stack.StackBranch{
+				{Name: "feature-a", Parent: "main"},
+			},
+			prCache: make(map[string]*github.PRInfo),
+			setupMocks: func(mockGit *testutil.MockGitClient) {
+				mockGit.On("IsAncestor", "feature-a", "origin/main").Return(true, nil)
+			},
+			expectedIssues: 1,
+		},
 	}
 
 	for _, tt := range tests {
diff --git a/cmd/sync.go b/cmd/sync.go
index 4e1d1a4..3ac1e81 100644
--- a/cmd/sync.go
+++ b/cmd/sync.go
@@ -508,6 +508,24 @@ func runSync(gitClient git.GitClient, githubClient github.GitHubClient, syncRemo
 			}
 			fmt.Println()
 			continue
+		} else if _, exists := prCache[branch.Name]; !exists {
+			// No PR found - check if branch was merged via git history
+			remoteBase := syncRemote + "/" + baseBranch
+			if merged, err := gitClient.IsAncestor(branch.Name, remoteBase); err == nil && merged {
+				fmt.Printf("%s Skipping %s (merged into %s, detected via git history)...\n", progress, ui.Branch(branch.Name), ui.Branch(baseBranch))
+				fmt.Printf("  Removing from stack tracking...\n")
+				configKey := fmt.Sprintf("branch.%s.stackparent", branch.Name)
+				if err := gitClient.UnsetConfig(configKey); err != nil {
+					fmt.Fprintf(os.Stderr, "  Warning: failed to remove stack config: %v\n", err)
+				} else {
+					fmt.Printf("  %s Removed. You can delete this branch with: %s\n", ui.SuccessIcon(), ui.Command(fmt.Sprintf("git branch -d %s", branch.Name)))
+				}
+				if branch.Name == originalBranch {
+					originalBranchMerged = true
+				}
+				fmt.Println()
+				continue
+			}
 		}
 
 		fmt.Printf("\n%s %s\n", progress, ui.Branch(branch.Name))
@@ -515,11 +533,22 @@ func runSync(gitClient git.GitClient, githubClient github.GitHubClient, syncRemo
 		// Check if parent PR is merged
 		oldParent := "" // Track old parent for --onto rebase
 		parentPR := prCache[branch.Parent]
+		parentMergedViaGit := false
 		if parentPR != nil && parentPR.State == "MERGED" {
 			fmt.Printf("  Parent PR #%d has been merged\n", parentPR.Number)
+			oldParent = branch.Parent
+		} else if parentPR == nil && branch.Parent != baseBranch {
+			// No PR found for parent - check if parent was merged via git history
+			remoteBase := syncRemote + "/" + baseBranch
+			if merged, err := gitClient.IsAncestor(branch.Parent, remoteBase); err == nil && merged {
+				fmt.Printf("  Parent %s appears merged into %s (detected via git history)\n", ui.Branch(branch.Parent), ui.Branch(baseBranch))
+				oldParent = branch.Parent
+				parentMergedViaGit = true
+			}
+		}
 
+		if oldParent != "" {
 			// Save old parent for --onto rebase
-			oldParent = branch.Parent
 
 			// Update parent to grandparent
 			grandparent := gitClient.GetConfig(fmt.Sprintf("branch.%s.stackparent", branch.Parent))
@@ -534,6 +563,16 @@ func runSync(gitClient git.GitClient, githubClient github.GitHubClient, syncRemo
 			} else {
 				branch.Parent = grandparent
 			}
+
+			// If parent was detected as merged via git (no PR), also remove it from stack tracking
+			if parentMergedViaGit {
+				parentConfigKey := fmt.Sprintf("branch.%s.stackparent", oldParent)
+				if err := gitClient.UnsetConfig(parentConfigKey); err != nil {
+					if git.Verbose {
+						fmt.Fprintf(os.Stderr, "  Note: could not remove stack config for %s: %v\n", oldParent, err)
+					}
+				}
+			}
 		}
 
 		// Checkout the branch
diff --git a/cmd/sync_test.go b/cmd/sync_test.go
index 42c78ea..17bafee 100644
--- a/cmd/sync_test.go
+++ b/cmd/sync_test.go
@@ -44,6 +44,8 @@ func TestRunSyncBasic(t *testing.T) {
 		// Parallel operations
 		mockGit.On("FetchRemote", "origin").Return(nil)
 		mockGH.On("GetPRsForBranches", mock.Anything).Return(make(map[string]*github.PRInfo))
+		// Git-based merge detection (no branches are merged)
+		mockGit.On("IsAncestor", mock.Anything, mock.Anything).Return(false, nil).Maybe()
 		// Check if any branches in the current stack are in worktrees
 		mockGit.On("GetWorktreeBranches").Return(make(map[string]string), nil)
 		mockGit.On("GetCurrentWorktreePath").Return("/Users/test/repo", nil)
@@ -129,6 +131,8 @@ func TestRunSyncMergedParent(t *testing.T) {
 			"feature-a": testutil.NewPRInfo(1, "MERGED", "main", "Feature A", "url"),
 		}
 		mockGH.On("GetPRsForBranches", mock.Anything).Return(prCache)
+		// Git-based merge detection fallback (for branches without PRs)
+		mockGit.On("IsAncestor", mock.Anything, mock.Anything).Return(false, nil).Maybe()
 
 		mockGit.On("GetWorktreeBranches").Return(make(map[string]string), nil)
 		mockGit.On("GetCurrentWorktreePath").Return("/Users/test/repo", nil)
@@ -285,6 +289,8 @@ func TestRunSyncStashHandling(t *testing.T) {
 
 		mockGit.On("FetchRemote", "origin").Return(nil)
 		mockGH.On("GetPRsForBranches", mock.Anything).Return(make(map[string]*github.PRInfo))
+		// Git-based merge detection (no branches are merged)
+		mockGit.On("IsAncestor", mock.Anything, mock.Anything).Return(false, nil).Maybe()
 
 		mockGit.On("GetWorktreeBranches").Return(make(map[string]string), nil)
 		mockGit.On("GetCurrentWorktreePath").Return("/Users/test/repo", nil)
@@ -348,6 +354,8 @@ func TestRunSyncErrorHandling(t *testing.T) {
 
 		mockGit.On("FetchRemote", "origin").Return(nil)
 		mockGH.On("GetPRsForBranches", mock.Anything).Return(make(map[string]*github.PRInfo))
+		// Git-based merge detection (no branches are merged)
+		mockGit.On("IsAncestor", mock.Anything, mock.Anything).Return(false, nil).Maybe()
 
 		mockGit.On("GetWorktreeBranches").Return(make(map[string]string), nil)
 		mockGit.On("GetCurrentWorktreePath").Return("/Users/test/repo", nil)
@@ -402,6 +410,8 @@ func TestRunSyncErrorHandling(t *testing.T) {
 
 		mockGit.On("FetchRemote", "origin").Return(nil)
 		mockGH.On("GetPRsForBranches", mock.Anything).Return(make(map[string]*github.PRInfo))
+		// Git-based merge detection (no branches are merged)
+		mockGit.On("IsAncestor", mock.Anything, mock.Anything).Return(false, nil).Maybe()
 
 		mockGit.On("GetWorktreeBranches").Return(make(map[string]string), nil)
 		mockGit.On("GetCurrentWorktreePath").Return("/Users/test/repo", nil)
@@ -537,6 +547,8 @@ func TestRunSyncResume(t *testing.T) {
 
 		mockGit.On("FetchRemote", "origin").Return(nil)
 		mockGH.On("GetPRsForBranches", mock.Anything).Return(make(map[string]*github.PRInfo))
+		// Git-based merge detection (no branches are merged)
+		mockGit.On("IsAncestor", mock.Anything, mock.Anything).Return(false, nil).Maybe()
 
 		mockGit.On("GetWorktreeBranches").Return(make(map[string]string), nil)
 		mockGit.On("GetCurrentWorktreePath").Return("/Users/test/repo", nil)
@@ -606,6 +618,8 @@ func TestRunSyncResume(t *testing.T) {
 
 		mockGit.On("FetchRemote", "origin").Return(nil)
 		mockGH.On("GetPRsForBranches", mock.Anything).Return(make(map[string]*github.PRInfo))
+		// Git-based merge detection (no branches are merged)
+		mockGit.On("IsAncestor", mock.Anything, mock.Anything).Return(false, nil).Maybe()
 
 		mockGit.On("GetWorktreeBranches").Return(make(map[string]string), nil)
 		mockGit.On("GetCurrentWorktreePath").Return("/Users/test/repo", nil)
@@ -694,6 +708,8 @@ func TestRunSyncAutoConfiguresMissingStackparent(t *testing.T) {
 		// Parallel operations
 		mockGit.On("FetchRemote", "origin").Return(nil)
 		mockGH.On("GetPRsForBranches", mock.Anything).Return(make(map[string]*github.PRInfo))
+		// Git-based merge detection (no branches are merged)
+		mockGit.On("IsAncestor", mock.Anything, mock.Anything).Return(false, nil).Maybe()
 
 		// Worktree checks
 		mockGit.On("GetWorktreeBranches").Return(make(map[string]string), nil)
@@ -774,6 +790,8 @@ func TestRunSyncNoUniqueCommits(t *testing.T) {
 		// Parallel operations
 		mockGit.On("FetchRemote", "origin").Return(nil)
 		mockGH.On("GetPRsForBranches", mock.Anything).Return(make(map[string]*github.PRInfo))
+		// Git-based merge detection (no branches are merged)
+		mockGit.On("IsAncestor", mock.Anything, mock.Anything).Return(false, nil).Maybe()
 		// Check if any branches in the current stack are in worktrees
 		mockGit.On("GetWorktreeBranches").Return(make(map[string]string), nil)
 		mockGit.On("GetCurrentWorktreePath").Return("/Users/test/repo", nil)
@@ -967,6 +985,8 @@ func TestRunSyncWithUpstreamRemote(t *testing.T) {
 		// Also fetch origin since syncRemote != "origin"
 		mockGit.On("Fetch").Return(nil)
 		mockGH.On("GetPRsForBranches", mock.Anything).Return(make(map[string]*github.PRInfo))
+		// Git-based merge detection (no branches are merged)
+		mockGit.On("IsAncestor", mock.Anything, mock.Anything).Return(false, nil).Maybe()
 		// Worktree checks
 		mockGit.On("GetWorktreeBranches").Return(make(map[string]string), nil)
 		mockGit.On("GetCurrentWorktreePath").Return("/Users/test/repo", nil)
@@ -1060,6 +1080,8 @@ func TestRunSyncSkipsWorktreeBranches(t *testing.T) {
 		// Parallel operations
 		mockGit.On("FetchRemote", "origin").Return(nil)
 		mockGH.On("GetPRsForBranches", mock.Anything).Return(make(map[string]*github.PRInfo))
+		// Git-based merge detection (no branches are merged)
+		mockGit.On("IsAncestor", mock.Anything, mock.Anything).Return(false, nil).Maybe()
 
 		// feature-b is in another worktree
 		mockGit.On("GetWorktreeBranches").Return(map[string]string{
@@ -1175,3 +1197,142 @@ func TestRunPostSyncInstall(t *testing.T) {
 		assert.Equal(t, "pnpm", detected.command)
 	})
 }
+
+func TestRunSyncGitBasedMergeDetection(t *testing.T) {
+	testutil.SetupTest()
+	defer testutil.TeardownTest()
+
+	t.Run("removes branch from stack when merged via git history (no PR)", func(t *testing.T) {
+		mockGit := new(testutil.MockGitClient)
+		mockGH := new(testutil.MockGitHubClient)
+
+		// Setup: no existing sync state
+		mockGit.On("GetConfig", "stack.sync.stashed").Return("")
+		mockGit.On("GetConfig", "stack.sync.originalBranch").Return("")
+		mockGit.On("GetCurrentBranch").Return("feature-b", nil)
+		mockGit.On("SetConfig", "stack.sync.originalBranch", "feature-b").Return(nil)
+		mockGit.On("IsWorkingTreeClean").Return(true, nil)
+		mockGit.On("GetConfig", "branch.feature-b.stackparent").Return("feature-a")
+		mockGit.On("GetConfig", "stack.baseBranch").Return("").Maybe()
+		mockGit.On("GetDefaultBranch").Return("main").Maybe()
+
+		stackParents := map[string]string{
+			"feature-a": "main",
+			"feature-b": "feature-a",
+		}
+		mockGit.On("GetAllStackParents").Return(stackParents, nil).Maybe()
+
+		// No PRs found at all
+		mockGit.On("FetchRemote", "origin").Return(nil)
+		mockGH.On("GetPRsForBranches", mock.Anything).Return(make(map[string]*github.PRInfo))
+
+		mockGit.On("GetWorktreeBranches").Return(make(map[string]string), nil)
+		mockGit.On("GetCurrentWorktreePath").Return("/Users/test/repo", nil)
+		mockGit.On("GetRemoteBranchesSet").Return(map[string]bool{
+			"main":      true,
+			"feature-a": true,
+			"feature-b": true,
+		})
+
+		// feature-a: no PR, but IsAncestor returns true → merged via git history
+		mockGit.On("IsAncestor", "feature-a", "origin/main").Return(true, nil)
+		// Remove feature-a from stack
+		mockGit.On("UnsetConfig", "branch.feature-a.stackparent").Return(nil)
+
+		// feature-b: no PR, not merged via git
+		mockGit.On("IsAncestor", "feature-b", "origin/main").Return(false, nil)
+
+		// feature-b's parent (feature-a) has no PR, parent merged via git
+		// IsAncestor("feature-a", "origin/main") already mocked above → true
+
+		// Reparent feature-b from feature-a to main
+		mockGit.On("GetConfig", "branch.feature-a.stackparent").Return("main")
+		mockGit.On("SetConfig", "branch.feature-b.stackparent", "main").Return(nil)
+		// Also remove parent from stack tracking (called again for parent cleanup)
+		mockGit.On("UnsetConfig", "branch.feature-a.stackparent").Return(nil)
+
+		// Process feature-b: checkout, rebase onto origin/main (new parent)
+		mockGit.On("CheckoutBranch", "feature-b").Return(nil)
+		mockGit.On("GetCommitHash", "feature-b").Return("def456", nil)
+		mockGit.On("GetCommitHash", "origin/feature-b").Return("def456", nil)
+		mockGit.On("FetchBranchFromRemote", "origin", "main").Return(nil)
+		// --onto rebase since parent was merged
+		mockGit.On("RebaseOnto", "origin/main", "feature-a", "feature-b").Return(nil)
+		mockGit.On("FetchBranch", "feature-b").Return(nil)
+		mockGit.On("PushWithExpectedRemote", "feature-b", "def456").Return(nil)
+
+		// Return to original branch
+		mockGit.On("CheckoutBranch", "feature-b").Return(nil)
+		// Clean up sync state
+		mockGit.On("UnsetConfig", "stack.sync.stashed").Return(nil)
+		mockGit.On("UnsetConfig", "stack.sync.originalBranch").Return(nil)
+		mockGit.On("GetConfig", "stack.postSyncInstall").Return("false").Maybe()
+
+		err := runSync(mockGit, mockGH, "origin")
+
+		assert.NoError(t, err)
+		mockGit.AssertExpectations(t)
+		mockGH.AssertExpectations(t)
+	})
+
+	t.Run("branch not merged via git is processed normally", func(t *testing.T) {
+		mockGit := new(testutil.MockGitClient)
+		mockGH := new(testutil.MockGitHubClient)
+
+		// Setup: no existing sync state
+		mockGit.On("GetConfig", "stack.sync.stashed").Return("")
+		mockGit.On("GetConfig", "stack.sync.originalBranch").Return("")
+		mockGit.On("GetCurrentBranch").Return("feature-a", nil)
+		mockGit.On("SetConfig", "stack.sync.originalBranch", "feature-a").Return(nil)
+		mockGit.On("IsWorkingTreeClean").Return(true, nil)
+		mockGit.On("GetConfig", "branch.feature-a.stackparent").Return("main")
+		mockGit.On("GetConfig", "stack.baseBranch").Return("").Maybe()
+		mockGit.On("GetDefaultBranch").Return("main").Maybe()
+
+		stackParents := map[string]string{
+			"feature-a": "main",
+		}
+		mockGit.On("GetAllStackParents").Return(stackParents, nil).Maybe()
+
+		// No PRs found
+		mockGit.On("FetchRemote", "origin").Return(nil)
+		mockGH.On("GetPRsForBranches", mock.Anything).Return(make(map[string]*github.PRInfo))
+		// Git-based merge detection (no branches are merged)
+		mockGit.On("IsAncestor", mock.Anything, mock.Anything).Return(false, nil).Maybe()
+
+		mockGit.On("GetWorktreeBranches").Return(make(map[string]string), nil)
+		mockGit.On("GetCurrentWorktreePath").Return("/Users/test/repo", nil)
+		mockGit.On("GetRemoteBranchesSet").Return(map[string]bool{
+			"main":      true,
+			"feature-a": true,
+		})
+
+		// feature-a: no PR, NOT merged via git either
+		mockGit.On("IsAncestor", "feature-a", "origin/main").Return(false, nil)
+
+		// Should process normally (no parent reparenting since parent is baseBranch)
+		mockGit.On("CheckoutBranch", "feature-a").Return(nil)
+		mockGit.On("GetCommitHash", "feature-a").Return("abc123", nil)
+		mockGit.On("GetCommitHash", "origin/feature-a").Return("abc123", nil)
+		mockGit.On("FetchBranchFromRemote", "origin", "main").Return(nil)
+		mockGit.On("GetUniqueCommitsByPatch", "origin/main", "feature-a").Return([]string{"abc123"}, nil)
+		mockGit.On("GetMergeBase", "feature-a", "origin/main").Return("main123", nil)
+		mockGit.On("GetCommitHash", "origin/main").Return("main123", nil)
+		mockGit.On("Rebase", "origin/main").Return(nil)
+		mockGit.On("FetchBranch", "feature-a").Return(nil)
+		mockGit.On("PushWithExpectedRemote", "feature-a", "abc123").Return(nil)
+
+		// Return to original branch
+		mockGit.On("CheckoutBranch", "feature-a").Return(nil)
+		// Clean up sync state
+		mockGit.On("UnsetConfig", "stack.sync.stashed").Return(nil)
+		mockGit.On("UnsetConfig", "stack.sync.originalBranch").Return(nil)
+		mockGit.On("GetConfig", "stack.postSyncInstall").Return("false").Maybe()
+
+		err := runSync(mockGit, mockGH, "origin")
+
+		assert.NoError(t, err)
+		mockGit.AssertExpectations(t)
+		mockGH.AssertExpectations(t)
+	})
+}
diff --git a/internal/git/git.go b/internal/git/git.go
index 2ffa30c..cb05bca 100644
--- a/internal/git/git.go
+++ b/internal/git/git.go
@@ -687,6 +687,25 @@ func (c *gitClient) ListWorktrees() ([]string, error) {
 	return paths, nil
 }
 
+// IsAncestor checks if commit is an ancestor of branch using git merge-base --is-ancestor.
+// Returns true if commit is an ancestor, false if not. Other exit codes return an error.
+func (c *gitClient) IsAncestor(commit, branch string) (bool, error) {
+	if Verbose {
+		fmt.Printf("  [git] merge-base --is-ancestor %s %s\n", commit, branch)
+	}
+	cmd := exec.Command("git", "merge-base", "--is-ancestor", commit, branch)
+	err := cmd.Run()
+	if err == nil {
+		return true, nil
+	}
+	if exitErr, ok := err.(*exec.ExitError); ok {
+		if exitErr.ExitCode() == 1 {
+			return false, nil
+		}
+	}
+	return false, fmt.Errorf("git merge-base --is-ancestor %s %s failed: %v", commit, branch, err)
+}
+
 // GetRemoteURL returns the URL of the specified remote (e.g., "origin")
 func (c *gitClient) GetRemoteURL(remoteName string) string {
 	return c.runCmdMayFail("remote", "get-url", remoteName)
diff --git a/internal/git/interface.go b/internal/git/interface.go
index 32352dc..8b6520d 100644
--- a/internal/git/interface.go
+++ b/internal/git/interface.go
@@ -54,4 +54,5 @@ type GitClient interface {
 	RemoveWorktree(path string) error
 	ListWorktrees() ([]string, error)
 	GetRemoteURL(remoteName string) string
+	IsAncestor(commit, branch string) (bool, error)
 }
diff --git a/internal/testutil/mocks.go b/internal/testutil/mocks.go
index 0eaec64..56c700f 100644
--- a/internal/testutil/mocks.go
+++ b/internal/testutil/mocks.go
@@ -276,6 +276,11 @@ func (m *MockGitClient) GetRemoteURL(remoteName string) string {
 	return args.String(0)
 }
 
+func (m *MockGitClient) IsAncestor(commit, branch string) (bool, error) {
+	args := m.Called(commit, branch)
+	return args.Bool(0), args.Error(1)
+}
+
 // MockGitHubClient is a mock implementation of github.GitHubClient for testing
 type MockGitHubClient struct {
 	mock.Mock