Malum prohibitum can be defined as
An act which is immoral because it is illegal; not necessarily illegal because it is immoral.
while malum in se can be defined as
An innately immoral act, regardless of whether it is forbidden by law. Examples include adultery, theft, and murder.
A side-by-side comparison is given here:
Legal scholars have used the terms mala prohibita and mala in se to draw the distinction between legally proscribed and morally proscribed offenses. The former are those offenses that are wrong simply because there exist formal, codified rules prohibiting them. Efforts to define mala in se, on the other hand, have resulted in vague, often conflicting meanings that leave the analyst with little but examples to serve as definitions. As a result, some have argued that the distinctions mala in se and mala prohibita be abandoned altogether. If one examines mala in se from an equity theoretical viewpoint, incorporating the concepts of intent and harm, it may be possible to arrive at a more understandable and useful concept.
In theory, the two are easy to distinguish, but in cases of, say, statutory rape, the differences fade away.