Crop depredation by brown bears (Ursus arctos) in Hokkaido, Japan, has increased over the past 2 decades. With increased depredation, the number of permits issued and the removal of conflict animals have also increased. We hypothesized that peripheral areas adjacent to agricultural lands represent attractive sink-like habitat because of the association between abundant high-quality anthropogenic food resources and high levels of human-induced mortality by nuisance control. We used an allopatric distribution of mitochondrial DNA (mtDNA) haplotypes in females to distinguish core from peripheral habitat; nuisance control for female bears was 2× greater in the periphery. Using these definitions, we investigated 85 male mtDNA haplotypes recovered from dead bears from eastern Hokkaido (1996–2008) and classified the birthplace for 64. Of these, 14 of 31 born in core were killed in periphery, whereas 5 of 33 born in periphery died in core. In periphery, the largest proportion of males killed occurred during early summer (mating season); for females, the largest proportion was in late summer (period of greatest crop damage). We also documented a significant increase in the number of males killed in the periphery since late 1990s. Timing of mortalities suggested that males were attracted to the periphery for both mating opportunities and by abundant anthropogenic food resources. Because our results suggest a directional flow of males from core to periphery, we suspected (although did not document) a net loss of residents from core. If reproduction was unable to compensate, unregulated control killing could eventually result in a decline in the numbers of males residing in the core. Our findings demonstrate an important application of mtDNA analyses as well as how source–sink dynamics can differentially affect males and females because of varying behavioral traits such as home range size and dispersal characteristics.