Increasing human impacts on the Kenai Peninsula, Alaska, have raised questions about potential implications for genetic diversity and population structure of local taxa. Black bears (Ursus americanus) occupy most of the Kenai Peninsula and are currently a species of public interest and management focus. In this study, we use 13 nuclear DNA (nDNA) microsatellite loci and sequence data from the mitochondrial DNA (mtDNA) control region to investigate population structure and phylogeographic patterns in black bears on the Kenai and surrounding mainland. We used both aspatial and spatial Bayesian assignment models to evaluate nDNA genetic structure and cluster individuals into genetically distinct groups. Substantial population substructure was detected, indicating restricted gene flow in recent generations as well as signatures of past barriers between the Kenai and mainland. We identified 3 genetically distinct groups that cluster geographically in the Kenai Peninsula, Alaskan mainland, and Prince William Sound areas. Connectivity among genetic groups was moderate, with F_st values ranging from 0.07 to 0.12. Five mtDNA haplotypes were detected, 2 of which were primarily restricted to the Kenai. Our results provide important information about current levels of genetic diversity and connectivity among black bears on the Kenai Peninsula and will provide a baseline for future monitoring.