For many years, researchers have speculated that fin whales are year-round residents in the Sea of Cortez (= Gulf of California). Previous work by Berube and co-workers has shown that the degree of genetic diversity among fin whales in the Sea of Cortez at nuclear and mitochondrial loci is highly reduced. However, the relatively unobstructed connection with the North Pacific Ocean argues that Sea of Cortez fin whales are part of a much larger eastern North Pacific population given the extensive migratory ranges observed in fin whales and baleen whales in general. The low degree of genetic variation might thus simply be due to historic fluctuations in the effective population size of an eastern North Pacific population. In order to test if the reduced genetic variation detected among fin whales in the Sea of Cortez is due to small population size or a past bottleneck in an otherwise large eastern North Pacific population, we analyzed the geographic distribution of genetic variation at a single mitochondrial (control region) and 16 nuclear loci in samples collected from fin whales in the eastern North Pacific (n = 12) as well as the Sea of Cortez (n = 77). Our results showed that fin whales observed in the Sea of Cortez constitute a highly isolated and thus evolutionary unique population, which warrants special conservation measures given the current low estimate of abundance of approximately 400 individuals.