The Formosan black bear (Ursus thibetanus formosanus, FBB) is an endangered subspecies of Asiatic black bear, geographically isolated in Taiwan from 6 other subspecies on the Asian continent and in Japan. Data on the genetic diversity and structure of wild FBB are lacking, though 2 potential hotspots for FBB occurrence have been identified; Yushan National Park (YNP) and Dasyueshan National Forest Recreation Area (DSY). Elucidating species' genetic structure can help assess the potential risks of population fragmentation and isolation that threaten FBB. Here, we employed 8 FBB-derived microsatellite loci to genotype 139 individuals from fecal samples collected in YNP, 20 captured individuals from both study areas, and 1 fecal sample from DSY, during 2009–2019. The marker set featured high polymorphic information content (mean > 0.699) and appropriate probability of identity (combined P(ID) < 0.0001) for individual identification. We detected high heterozygosity and no evidence of inbreeding in YNP, but the 2 subpopulations presented significant genetic differentiation. All DSY samples were assigned to one genetic cluster or phylogenetic clade, indicating that the DSY subpopulation is monophyletic. However, members of the YNP subpopulation were allocated to diverse lineages, and some YNP samples were partly assigned to the same cluster or clade as DSY individuals. We discuss potential evolutionary scenarios in which the observed population genetic structuring may have evolved. Based on our genetic results, the DSY and YNP subpopulations should be considered 2 separate management units and gene flow between both parts should be promoted.