The werewolf genocide was an attempt by the Volturi to wipe out the Children of the Moon, started by Caius, after he was nearly killed by one. Caius became terrified of them all, and convinced the rest of the Volturi to help him drive them into extinction.
The actual events are largely unrecorded, but the Volturi nearly succeeded in making the werewolves extinct in Europe and Asia. It is unknown if they are found anywhere else, but it is implied that at least a small number of them still exist since James, Victoria and Laurent were hunting one in Siberia. Also since there are real-life myths about them in America it may be possible they still exist in large numbers there.
In Breaking Dawn, Caius made the mistake of assuming Jacob's pack and Sam's pack are Children of the Moon when they changed into wolves; Aro corrected him.
Outside the Saga
A werewolf genocide occurs in The Vampire Diaries as well, with the werewolves also being driven to near-extinction by vampires who saw them as a threat.