It looks like sun damage to me. The dark areas could be from something that was stuck to the deck, mold growing on it or anything else that may have shaded the area or held moisture.

What brand of boat is it? If it's a Valley or NDK, the gelcoat is probably thick enough that you can wet sand it and get back to the original color. See page 2 of my "Gelcoat repair and restoration album on Webshots at:

http://community.webshots.com/user/brian_nystrom-reg