Genocide

Genocide is the criminal act of destroying or attempting to destroy an entire race or culture.

Real Life Genocides

Genocide is actually a rather common theme in science fiction. A term used for genocide against a Non Human species is Xenocide.

In TNG "I, Borg", the crew of the USS Enterprise develop a weapon that could destroy the entire Borg civilization. They justify this action with the knowledge that the Borg will do the same to their own civilization if not stopped.
In ENT "Dear Doctor", Dr. Phlox discovers a cure for a plague that is killing the Valakian race, but he decides not to give it to them because he thinks the Valakians are blocking the evolution of the Menk race, who share the planet with the Valakians. Captain Archer approves of the decision.
The destruction of Alderaan in Star Wars may or may not qualify. The mass murder of billions is a heinous crime itself, but Alderaan was inhabited primarily by humans, and there remained no shortage of planets inhabited by humans in the Empire. If Alderaan had a unique culture that was not found on other planets in the Empire, however, its destruction would qualify.
In Warhammer 40,000 forces of the Imperium of Man often commit genocide against non humans and religious deviants.
In Halo, the religious alien alliance called the Covenant seeks to wipe out humanity.