Elucidating how demography and contemporary landscape features regulate functional connectivity and diversity is crucial to implementing effective conservation strategies, especially in highly fragmented landscapes. We analyzed the impacts of landscape features and demographic events on the dispersal and genetic structure of a locally endangered carnivore, the leopard cat (Prionailurus bengalensis), across subtropical Taiwan. We genotyped 184 samples from both human-impacted and natural habitats using 12 nuclear microsatellites and a mitochondrial marker. Bayesian analyses revealed a recent population decline within the past 200 years, and a current genetic hotspot appears to have arisen from interbreeding between previously diverged populations. Genetic clustering and resistance surface modeling support the notion that the population structure is influenced by manufactured linear and natural topographical features. We employed a landscape optimization procedure using two genetic distances to reveal that highways and elevation are the most significant barriers affecting leopard cat connectivity. Niche modeling indicated that low temperature is a primary factor limiting leopard cat occurrence, potentially explaining why their resistance to movement is positively correlated with elevation. Utilizing an ensemble approach, we predict that suitable leopard cat habitat will shrink northward and towards higher more rugged altitudes. Our study provides genetic evidence that anthropogenic landscape features compromise the connectivity and persistence of a vagile carnivore that is under severe pressure from habitat loss and human activities. Our findings serve as a model for landscape genetic studies of island carnivores in subtropical regions, aimed at understanding how manufactured landscapes affect intra-species diversity and dispersal.