The Lower Keys marsh rabbit (LKMR, Sylvilagus palustris hefneri), a marsh rabbit subspecies endemic to the Lower Keys, Florida was protected in 1990, however, populations continue to decline despite recovery efforts. We hypothesized ongoing habitat loss and fragmentation due to succession and hardwood encroachment has lead to increased edge, reduced habitat quality, and increased activity by native raccoons (Procyon lotor). These factors reduce the suitability of patches in a later successional state, thus threatening LKMR recovery and metapopulation persistence. We surveyed 150 LKMR patches in 2008, tallying adult and juvenile rabbit pellets, estimating measures of habitat succession and quality (woody and herbaceous ground cover, distribution of herbaceous species) and recording raccoon activity (number of raccoon signs). We calculated patch edge (patch shape index) using ArcGIS. We evaluated the relationship between patch and habitat attributes and LKMR using regression analysis and model selection. We found both adult and juvenile LKMR pellet counts were lower in patches with higher shape indices and higher in patches with greater occurrence of bunchgrasses and forbs. We also found adult LKMR pellet counts were lower in patches with higher raccoon activity. Our results suggest patch edge, habitat succession and quality, and raccoons pose a threat to the persistence and recovery of LKMR populations. Recovery efforts should focus on reducing these trends through habitat management and raccoon removal implemented in carefully controlled experiments with proper monitoring. Measures of patch and habitat attributes important to LKMR should be incorporated into long-term metapopulation monitoring and used to evaluate recovery actions.