My 14 week old puppy is having green dicharge from his penis? What could be the problem.

It's normal for small amounts of discharge, however, if your dog's discharge is really greenish, and you've never noticed discharge of that color before, it's likely the discharge is caused by bacteria, and dog has an infection which can be easily cleared up with an antibiotic.

I suggest going to the vet and having it confirmed, as it can be a more serious issue such as balanoposthitis:

Balanoposthitis

However, if your puppy seems relatively healthy and is eating/pooping/playing, a simple visit to the vet should be helpful.

I agree with Sneezy, a trip to the vet is in order.