Git uses the git configuration file to set the colors. Typlically your global .gitconfig file is located in your home directory.
Here is an example of my .gitconfig file and how I set the git color status.
Git allows you to set the color for: color.branch color.diff color.interactive color.status
Here are some further details on git colors: http://git-scm.com/book/en/Customizing-Git-Git-Configuration#Colors-in-Git