Aim When introduced species invade new environments, they often overlap with native species currently occupying those spaces, either spatially through suitable habitat or environmentally through their realized niches. The goal of this research is to determine the overlap between native New England cottontail (Sylvilagus transitionalis) and introduced eastern cottontail (Sylvilagus floridanus) to identify potential areas of invasion by the eastern cottontail and potential areas of refuge for New England cottontail from eastern cottontail. Location Connecticut, USA Methods Using presence data from a regional, standardized monitoring protocol, we developed habitat suitability models using Maxent and conducted niche overlap analyses using Principal Component Analysis. We used several covariates that reflected proximity to habitat characteristics, such as young forest, shrubland, and understory, as well as proximity to threats, such as development. We also included topographic and climatic covariates. We used the Guidos software to categorize the spatial arrangement of young forest, shrubland, and understory vegetation. Results We found that the overlap in both niches and suitable habitat was high for two species. Only areas of low precipitation and high elevation shifted niches in favor of New England cottontail. We also found that habitat suitability for New England cottontail was higher when patches of mature forest without understory were within complexes of young forest, shrubland, and mature forest with understory. Main Conclusions Increasing habitat heterogeneity could improve the habitat suitability of existing patches or create new patches for New England cottontail. However, habitat management alone is likely not enough to discourage eastern cottontail, thus direct species management such as removal of eastern cottontail and augmentation of New England cottontail populations should be explored.