Sylvilagus aquaticus (Swamp Rabbit) is an imperiled species in Missouri that inhabits highly fragmented bottomland forested habitats in the southeastern portion of the state. Between 2010 and 2012, we conducted repeated, extensive presence—absence winterlatrine surveys in 15 counties to document their distribution. We compared our results to those of 2 previous winter-latrine surveys (2001–2002 and 1991–1992) conducted at the same sites. In addition, we used the Program MARK to estimate detection probability and site occupancy, and evaluate the influence of survey-site size on detectability and occupancy, and temperature at the time of the survey on detectability. We located 264 of 278 survey sites that were first surveyed in 1991, but could only survey 211. We detected Swamp Rabbits at 144 of 211 sites in 12 counties yielding a naïve occupancy estimate of 0.68. This estimate was higher than reported by both previous surveys: 0.53 in 2001–2002 and 0.40 in 1991–1992. Using occupancy modeling for the 2010–2012 survey, the estimated detection probability was 0.89 (SE = 0.02) and site occupancy was 0.70 (SE = 0.03). As expected, the size of a survey site influenced both detectability of and occupancy by Swamp Rabbits, and temperature influenced detectability. As the size of a site increased, both detectability and occupancy increased, and detectability increased as temperature decreased. Swamp Rabbits continue to occur in 13 counties and occupy fragmented, sometimes isolated blocks of bottomland forested habitat across the Mississippi River Alluvial Basin and along some Ozark Highlands streams.