Island species have long been considered an important system for investigating evolutionary forces leading to divergence. The Island spotted skunk (Spilogale gracilis amphiala) is an endemic insular carnivore found on two of the California Channel Islands: 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 spp.), leading some to suggest that spotted skunks may have arrived on the Channel Islands <200 years ago. However, studies using microsatellite and mitochondrial markers found significant differences among the two island populations and mainland populations. Still, these markers were insufficient to precisely estimate when island skunks diverged from one another and their mainland relative. To address this question as well as consequences for genetic diversity and inbreeding, we used a combination of whole genome sequencing on six individuals and reduced representation sequencing on 72 individuals. We estimated genomic diversity, inbreeding, and timing of population divergence. Our results support the antiquity of island spotted skunks, showing high genomic differentiation among all three populations, and both lower diversity and increased inbreeding in island populations. Additionally, demographic trajectories of island and mainland populations diverged >10,000 years ago.