mmmm you need to talk to him about it if you have not already. Chances are hes pretty in tune with his Johnson. I know If i saw something on my penis I would definitely find out what it is ASAP.
If he hasnt had it forever I doubt its a birthmark, if it is...your question will be answered in two seconds.
Ask him some questions, I would be shocked if he didnt know what it was or wasnt actively trying to figure out what it is.