Mackerels, tunas, and billfishes (suborder Scombroidei and Teleostei) provide an ideal taxonomic context in which to examine the evolution of endothermy. Multiple origins and diverse strategies for endothermy exist among these fish. Here a molecular phylogeny of the Scombroidei has been determined by direct sequencing of a portion of the mitochondrial cytochrome b gene. The distribution of endothermic species within this proposed genealogy indicates that the ability to warm the brain and retina arose independently in three lineages, each time in association with a movement into colder water. This suggests that the evolution of cranial endothermy in fish was selected in order to permit thermal niche expansion and not selected for increased aerobic capacity.