Island species have long been considered an important tool for understanding divergence and speciation, and to investigate the evolutionary forces driving DNA sequence evolution. The Island spotted skunk (Spilogale gracilis amphiala) is one example of an extremely rare endemic insular carnivore. Currently found on the two largest northern Channel Islands, Santa Rosa and Santa Cruz, island spotted skunk populations are morphologically nearly indistinguishable from one another and from their mainland counterpart, the western spotted skunk (S. gracilis microrhina, S. gracilis phenax). However, genetic studies that used microsatellites and mitochondrial DNA found significant genetic differences between the two island populations and between the islands and mainland populations, suggesting a longer evolutionary history of spotted skunks on the Channel Islands (Floyd et al. 2011; Bolas et al in review). To further investigate the evolutionary history of island spotted skunks and the forces driving their divergence we used whole genome sequencing to estimate current and historical population sizes, levels of inbreeding, and differentiation between each island and between the islands and mainland California.