Island species have long been considered an important tool for understanding speciation and to investigate evolutionary forces driving DNA sequence evolution. The Island spotted skunk (Spilogale gracilis amphiala) is an endemic insular carnivore found on two of the Channel Islands off the coast of southern California: Santa Rosa Island and Santa Cruz Island. Limited study of morphology found little differentiation between the island spotted skunks and their mainland counterpart, the western spotted skunk (S. gracilis microrhina, S. gracilis phenax), fueling an idea that spotted skunks arrived on the Channel Islands in the past two centuries. However, genetic studies using microsatellites and mitochondrial DNA found significant differences among the two island populations and mainland populations, suggesting a longer evolutionary history of spotted skunks on the islands. Still, the degree to which island spotted skunks are diverged from one another and from their mainland relative remain unclear. To further investigate the evolutionary history of island spotted skunks, we sequenced whole genomes of skunks from Santa Cruz Island, Santa Rosa Island, and the California mainland. Our results support the antiquity of island spotted skunks, showing high genomic differentiation between all three populations, lower diversity in island populations, and increased inbreeding in island populations.