Remove directory from git and local

You could checkout ‘master’ with both directories;

git rm -r one-of-the-directories // This deletes from filesystem
git commit . -m "Remove duplicated directory"
git push origin <your-git-branch> (typically 'master', but not always)

Remove directory from git but NOT local

As mentioned in the comments, what you usually want to do is remove this directory from git but not delete it entirely from the filesystem (local)

In that case use:

git rm -r --cached myFolder