Effective management of American black bears (Ursus americanus) requires an understanding of population demographics. In 2002, we obtained DNA from hair collected at barbed-wire traps to estimate black bear population size and study population genetics on Stockton (4,069 ha) and Sand (1,193 ha) islands at Apostle Islands National Lakeshore (AINL), Wisconsin. Hair samples also were collected from 2 nuisance bears on Oak Island. We analyzed 372 hair samples from Stockton and Sand islands collected on 4 occasions at about 14-day intervals. Genetic analysis of 6 microsatellite DNA markers resulted in 71 captures of 26 individuals on Stockton Island and 13 captures of 6 individuals on Sand Island. The estimated bear populations on Stockton and Sand islands were 26 (SE = 0.54, 95% CI [confidence interval] = 26–26) and 6 (SE = 0.60, 95% CI = 6–7) individuals, respectively. The estimated density on Stockton Island was 0.64 bears/km² and on Sand Island was 0.50 bears/km². Genetic variation within both island populations was higher (mean H_E ≥ 0.77) than could be maintained by populations of this size in isolation, suggesting substantial immigration from the mainland population occurred. Genetic assignment testing using log genotype likelihoods demonstrated sufficient variation between bear populations on Stockton and Sand islands to permit identification of natal origins. The 2 bears from Oak Island were genetically intermediate between Stockton and Sand islands. Islands within AINL contain small black bear populations of high density that are genetically distinct and apparently influenced by immigration from the mainland population.