American black bears (Ursus americanus) occur on numerous islands within the Apostle Islands National Lakeshore in Lake Superior, Wisconsin, USA, and provide an opportunity to better understand patterns in abundance and genetic structure among island populations. In 2002 and 2010, we derived genotypes from DNA obtained from hair samples collected at hair traps to estimate population abundance on Stockton (40.7 km²), Sand (11.9 km²), and Oak (20.6 km²; 2010 only) islands. We used Huggins closed-population mark–recapture models to estimate island-specific abundance and density. We used Program STRUCTURE and parentage analysis to examine inter-island population structure, migration patterns, and relatedness. In 2010, we estimated abundance on Stockton, Sand, and Oak islands to be 13.1 (95% CI = 12.4–13.8), 10.1 (95% CI = 9.3–11.0), and 18.1 (95% CI = 17.3–19.0) bears, with a density of 0.32, 0.85, and 0.88 bears/km², respectively. Whereas abundance on Sand Island increased 60% since 2002 (N = 6.3, 95% CI = 4.0–8.6), abundance on Stockton declined 50% (N = 26.3, 95% CI = 24.7–27.9), including an 83% decline in detected females. Density on Oak Island was the highest reported in Wisconsin, although we identified 13 individuals as likely mates or offspring of a single male. We identified 4 genetic groups, corresponding to Stockton, Sand, Oak, and Mainland ancestry. No individuals on Stockton or Sand islands were assigned ancestry from another island, whereas one male on Oak Island was assigned Stockton ancestry. We detected individuals of predominately Mainland ancestry on all but Hermit Island, suggesting a high rate of immigration from the mainland. We suggest these islands can support high bear densities, but may undergo rapid shifts in sex-specific abundance. Genetic connectivity appears maintained by male-mediated gene flow, but a small number of wide-ranging females may sustain inter-island population viability.