The New England cottontail (Sylvilagus transitionalis) has suffered from extensive loss and fragmentation of its habitat and is now a species of conservation priority in the northeastern United States. Remnant New England cottontail populations currently occur in five geographically disjunct locations: southern Maine and southeastern New Hampshire (MENH); the Merrimack Valley in central New Hampshire (NH-MV); Cape Cod, Massachusetts (CC); parts of eastern Connecticut and Rhode Island (CTRI); and western Connecticut, southeastern New York and southwestern Massachusetts (CTNY). We used microsatellite genotyping to discern patterns of population structure, genetic variability, and demographic history across the species’ range and to assess whether the observed patterns are a consequence of recent habitat loss and fragmentation. Our findings show that the geographic populations are highly differentiated (overall F ST = 0.145; P < 0.001). Using Bayesian clustering analyses, we identified five genetic clusters, which corresponded closely to the geographic populations, but grouped MENH & NH-MV together (ME/NH) and identified an isolated population in eastern Connecticut (Bluff Point). The genetic clusters showed little evidence of recent gene flow and are highly influenced by genetic drift. The CC and Bluff Point populations show signs they experienced a genetic bottleneck, whereas the ME/NH population shows evidence of ongoing decline. Populations in Bluff Point, CC, and ME/NH also show significantly reduced genetic variation relative to the other clusters (CTNY and CTRI without Bluff Point). Without immediate human intervention, the short-term persistence of New England cottontail populations in Maine, New Hampshire and Cape Cod is at great risk. Conservation efforts at this time should focus on within-population sustainability and eventually restoring connectivity among these isolated populations.