We investigated population densities and genetic structure of black bears at three national wildlife refuges (Great Dismal Swamp [GDSNWR], Pocosin Lakes [PLNWR], and Alligator River [ARNWR]). We derived density estimates from DNA samples collected noninvasively at each refuge for two consecutive summers. Hair samples were analyzed for individual identification using 6-7 microsatellite markers. Estimated densities were some of the highest reported in the literature and ranged from 0.56-0.63 bears/km2 at GDSNWR to 0.65-1.12 bears/km2 at ARNWR to 1.23-1.66 bears/km2 at PLNWR. Sex ratios were male-biased at all refuges. We also assessed genetic variability of bear populations at these refuges using 16 microsatellite markers for 40 bears at each refuge. Genetic variability was substantially high at all refuges compared to other bear populations in North America, with observed heterozygosities ranging from 0.6729 at GDSNWR to 0.7219 at ARNWR. FST and DS values were relatively low (0.0257-0.0895 and 0.0971-0.3640, respectively), suggesting that gene flow across the landscape is adequate to prevent high levels of genetic differentiation among refuge populations. Genetic statistics at GDSNWR compared to ARNWR and PLNWR (lower heterozygosity, higher FST and DS, etc.) suggest that this population is partially isolated, potentially due to geography (i.e., the Albemarle Sound) and urbanization (i.e., the towns of Suffolk and Chesapeake). U.S. Fish and Wildlife Service should consider maintenance of natural corridors to the south of ARNWR to ensure adequate gene flow among populations.