Go to the MonoDevelop syntax highlighting options panel and press the "New" button:
Enter a name and description for your new colour scheme, and pick the existing colour scheme on which you would like to base it:
Select your new colour scheme, and press the "Edit" button:
Now you can edit the colours of your new scheme:
Note : Some time you need to restart the MonoDevelop.
Note that you can export your scheme definition as a file using the buttons at the bottom of the syntax highlighting options panel, or import a scheme from a file. The schemes are defined using a simple XML format. However, beware that the filename must be of the form *Scheme.xml.