In Oregon, USA, bobcats on either side of the Cascade Mountain Range are recognized as distinct subspecies, with Lynx rufus fasciatus west and Lynx rufus pallescens east of the Cascades. These subspecies are currently managed for harvest as separate populations primarily because of substantial differences in regional pelt values. We used genetic data to determine whether bobcats in Oregon are subdivided into genetically discernible populations that support current regional management regulations. We collected 250 tissue samples from 12 a priori sampling districts, and generated data from 15 microsatellite markers and approximately 1 kB of mtDNA sequence. Results of clustering analyses based on the microsatellite data indicated strong support for the presence of 2 genetic populations, generally corresponding to the 2 subspecies. Analysis of molecular variance (AMOVA) indicated significant structure between the east and west regions, which accounted for 1.7% of the total variation in microsatellites. AMOVA based on the mtDNA sequences indicated significant structure between regions, accounting for 12.8% of the mtDNA variation. With both microsatellite and mtDNA data, we observed a significant pattern of isolation-by-distance, whereby geographically proximate sampling districts were more genetically similar than were more distant districts. We identified 21 putative migrants, individuals with genotypes more likely to have originated from the opposite region, showing that the Cascade Mountain Range apparently is not an absolute barrier to gene flow. Given the potential for differential harvest effort by region based on differences in pelt values and bobcat densities, and the vulnerability of bobcats to harvest, our results support the current management framework. © 2013 The Wildlife Society.