In fragmented habitat, population persistence depends in part on patch quality and patch size relative to home-range size. The imperiled New England cottontail (Sylvilagus transitionalis (Bangs, 1895)) is an obligate user of shrublands in the northeastern United States, a highly fragmented and declining ecosystem. New England cottontail conservation efforts have targeted habitat creation; however, efforts are hindered by a limited knowledge of seasonal space use and its relationship to habitat quality, which could help inform minimum patch-size requirements and implications of competition with non-native eastern cottontails (Sylvilagus floridanus (J.A. Allen, 1890)). To address these uncertainties, we modeled home-range areas for both species as a function of season, patch size, sex, and two indicators of forage and cover availability. Home range was generally inversely correlated with measures of forage and cover resources and the response differed by season and species and did not vary with patch size. Instead, inclusion of matrix habitat within home ranges increased with decreasing patch size, placing individuals within smaller patches at a high risk of mortality. These risks may be mitigated in patches >7 ha and absent in patches >20–25 ha where predicted inclusion of matrix is lower or absent.