The genetic variation within and between putative Killer whale (Orcinus orca) populations was examined by DNA fingerprinting nuclear genomes and sequencing the D-loop region of the mitochondrial genome. Mitochondrial DNA variation indicated that two sympatric populations in the northeastern Pacific were as genetically distinct as North Pacific populations from a South Atlantic population. The two sympatric populations are known to pursue different foraging strategies. DNA fingerprinting showed very low levels of variation within populations relative to comparisons between allopatric populations, suggesting inbreeding. These results are consistent with predictions about the genetic structure of Killer whale populations based on behavioural observations and variation in colour morphology.