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[FIXED] Error 'fatal: refusing to merge unrelated histories' in Git

Read Time: 3 min Updated: 2026-08-03

Quick Diagnostics

The error fatal: refusing to merge unrelated histories occurs when attempting to execute git pull or git merge between two Git repositories that do not share a common commit history. This frequently happens when you run git init locally while simultaneously creating a new repository on GitHub initialized with a README.md or .gitignore file.

Quick Solution (1 Minute): Execute the pull command with the allow flag: git pull origin main --allow-unrelated-histories

🚀 Step-by-Step Troubleshooting

Step 1: Force Merge Unrelated Histories

Open your terminal in your local project folder and run:

BASH 
git pull origin main --allow-unrelated-histories

(Replace main with master if your default branch uses the old naming).

This flag instructs Git to stitch together the history trees of both independent root commits.

Step 2: Resolve Any Merge Conflicts

If both the local and remote repos contain identical filenames (like README.md), Git will mark a conflict.

  1. Open the conflicted files in your code editor and select the content to keep.
  2. Stage the resolved files:
BASH 
git add .

Step 3: Complete Merge Commit and Push

Finish the merge process and upload the unified history to GitHub:

BASH 
git commit -m "Fix: Merge unrelated histories from remote and local"
git push origin main

Prevention Advice

Recommended security practices:

  • If you initialize a repo on GitHub with a README.md, always clone it to your machine (git clone <url>) rather than initializing locally with git init.
  • If you start locally with git init, create an empty repository on GitHub (do not select README or License options).