Resolve Git Unrelated Histories Error During Rebase

The “fatal: refusing to merge unrelated histories” error occurs when Git branches have no common commit history. To resolve this during rebase, use the --allow-unrelated-histories flag with your rebase command, like git rebase origin/development --allow-unrelated-histories. This flag, introduced in Git 2.9.0, allows Git to proceed with the rebase even when detecting unrelated histories.

Contents

• Understanding the Error
• Using the --allow-unrelated-histories Flag
• Alternative Solutions
• Step-by-Step Examples
• Troubleshooting Common Issues
• Best Practices

Understanding the Error

The “fatal: refusing to merge unrelated histories” error occurs when Git attempts to perform operations like rebase or merge on branches that don’t share any common commit history. This typically happens in several scenarios:

• When working with separate repositories that are later combined
• When creating orphan branches or starting new projects in the same repository
• When remotes are changed and branches have divergent histories
• When using git init followed by adding existing code without proper import

As GeeksforGeeks explains, “Without a shared history, Git cannot perform a rebase, merge, or any operation that relies on a common commit base.”

The additional error “Error redoing merge 1234deadbeef1234deadbeef” indicates that Git was attempting to reapply a merge commit but couldn’t find the appropriate base to apply it against due to the unrelated histories.

Using the --allow-unrelated-histories Flag

The --allow-unrelated-histories flag is the direct solution to this problem, introduced in Git 2.9.0 specifically to address this scenario. This flag instructs Git to proceed with the merge or rebase operation even when it detects that the branches have unrelated histories.

Basic Syntax

git rebase origin/development --allow-unrelated-histories

This command tells Git to:

1. Attempt to rebase your current branch onto origin/development
2. Allow the operation to proceed despite unrelated histories
3. Create a new merge commit if necessary

Alternative Command Variations

You can also use this flag with related commands:

# Using with git pull
git pull origin development --allow-unrelated-histories

# Using with git merge
git merge origin/development --allow-unrelated-histories

# Using with git pull --rebase
git pull origin development --rebase --allow-unrelated-histories

As SourceBae notes, “This forces Git to allow the merge of branches that do not share a common history, a behavior that is denied by default in Git.”

Alternative Solutions

While --allow-unrelated-histories is the most direct solution, there are alternative approaches that can resolve this issue:

1. Interactive Rebase

Interactive rebase allows you to manually connect the histories by rewriting the commit history:

git rebase -i origin/development

This gives you the ability to:

• Pick and reorder commits
• Squash multiple commits into one
• Edit commit messages
• Explicitly connect the histories

2. Patch-based Approach

Export commits from one branch as patches and apply them to another:

# Export commits as patches
git format-patch origin/development..HEAD

# Apply patches to the target branch
git checkout origin/development
git am < *.patch

3. Orphan Branch Approach

Create a new orphan branch and manually merge the histories:

git checkout --orphan new-branch
git merge --allow-unrelated-histories old-branch

Step-by-Step Examples

Scenario 1: Basic Rebase with Unrelated Histories

# Start with the error
git rebase origin/development
# fatal: refusing to merge unrelated histories

# Solution with the flag
git rebase origin/development --allow-unrelated-histories

Scenario 2: Handling Conflicts

When using --allow-unrelated-histories, conflicts are likely:

# Start the rebase with the flag
git rebase origin/development --allow-unrelated-histories

# Git will stop at conflicting files
# Edit the files to resolve conflicts
git add <resolved-file>
git rebase --continue

# If you need to abort
git rebase --abort

Scenario 3: Using with git pull

# Fetch the latest changes first
git fetch origin

# Then rebase with the flag
git rebase origin/development --allow-unrelated-histories

As Baeldung on Ops demonstrates, “use the option –allow-unrelated-histories after the git pull command.”

Troubleshooting Common Issues

“Error redoing merge” Message

If you encounter “Error redoing merge 1234deadbeef1234deadbeef”, it usually means:

1. The merge commit cannot be reapplied due to unrelated histories
2. Git needs manual intervention to resolve the merge conflict

Solution:

# Abort the current rebase
git rebase --abort

# Try a different approach
git merge --allow-unrelated-histories origin/development

Conflicts During Rebase

When conflicts occur during --allow-unrelated-histories rebase:

# 1. Resolve the conflicts in your editor
# 2. Stage the resolved files
git add <conflicted-file>

# 3. Continue the rebase
git rebase --continue

# 4. If you can't resolve, abort
git rebase --abort

Flag Not Recognized

If you’re using Git version < 2.9.0, the flag won’t be available:

# Check your Git version
git --version

# Upgrade Git if necessary
# For Ubuntu/Debian:
sudo apt update && sudo apt install git

# For macOS with Homebrew:
brew upgrade git

Best Practices

When to Use --allow-unrelated-histories

• Use it when you’re combining separate repositories or projects
• Use it when you’ve changed remotes and need to reconnect histories
• Use it when you’re working with orphan branches that need to be merged

When to Avoid --allow-unrelated-histories

• Avoid it when you’re working with established branches that should have a common history
• Avoid it when you’re unsure about the relationship between branches
• Avoid it as a first solution - investigate why histories are unrelated first

Post-Rebase Steps

After successfully using --allow-unrelated-histories:

# Verify the result
git log --oneline --graph

# Push to remote (force push may be needed)
git push origin your-branch --force-with-lease

# Consider cleaning up if appropriate
git branch -d old-branch

As Better Stack Community advises, “By using the --allow-unrelated-histories option, you’re explicitly telling Git to allow the merge or rebase operation even if the branches have unrelated histories.”

Conclusion

The “–allow-unrelated-histories” flag provides a straightforward solution to Git’s “fatal: refusing to merge unrelated histories” error during rebase operations. Key takeaways:

• Use git rebase origin/development --allow-unrelated-histories to resolve the error
• This flag, introduced in Git 2.9.0, allows rebase operations on branches without common history
• Be prepared to resolve conflicts manually after using this flag
• Consider alternative approaches like interactive rebase or patch-based merging for cleaner history
• Always verify the result after completing the operation

For your specific case with Git 2.9.0, the --allow-unrelated-histories flag should work perfectly since it was introduced in that version. If you encounter additional issues with merge commits, consider using git merge instead of git rebase with the same flag.

Sources

1. Git refusing to merge unrelated histories on rebase - Stack Overflow
2. How to Fix ‘fatal: refusing to merge unrelated histories’ During Git Rebase - OpenReplay Blog
3. How to Fix - Git Refusing to Merge Unrelated Histories on Rebase - GeeksforGeeks
4. Git refusing to merge unrelated histories on rebase - SourceBae
5. Git Refusing to Merge Unrelated Histories on Rebase - Better Stack Community
6. How To Handle Git Refusing To Merge Unrelated Histories On Rebase - Squash.io
7. How to resolve the Git error “refusing to merge unrelated histories” - Graphite.dev
8. How to Fix Git “Refusing to Merge Unrelated Histories” - Baeldung on Ops