I'm gonna have to go with cultural...not necessarily creation-belief based nor evolution-based.
I don't think the magical sky fairies ingrained conscience into man...nor do I believe it's an evolved trait, but rather, the ability to discern right from wrong is the result of cultural pressures. In cultures that have strong beliefs about what's right and what's wrong, conscience and guilt go hand-in-hand...Look at all the stories, movies, and jokes about "I survived a Jewish mother," or I survived a Catholic mother." Both religions are heavy on the guilt...which requires strong beliefs in conscience...
Many non-religious cultures, such as the American Indian tribes, had far less pressure about right and wrong...with little to no guilt passed down for right and wrong. If you did wrong, you may have been punished for it, but they didn't "lay a bunch of guilt trips" on you over it.
It's a learned behavior...it's pounded into us from the time we're children...by our parents, at school, at church (if you swing that way) and by society in general.