Sylvilagus palustris hefneri (Lower Keys Marsh Rabbit [LKMR]) is an endangered subspecies of marsh rabbit found only in the Lower Florida Keys. In September 2017, Hurricane Irma was measured as a Category 4 storm when it passed through the center of the LKMR range causing significant damage to human infrastructure and natural habitats. To assess the impact of Hurricane Irma to LKMR and its habitat, we compared pre- and post-hurricane monitoring data. Overall, 82% of LKMR habitat patches were abandoned, the average number of pellets per sampling plot decreased 94%, and average patch pellet density decreased by 84% following Hurricane Irma. Generally, pellets were found in plots with greater open cover, an intermediate amount of herbaceous and woody cover, and areas with more standing water post-Hurricane Irma. We also observed a slight decrease in signs of Procyon lotor (Raccoon) and Didelphis virginiana (Virginia Opossum). The decrease in rabbit pellets detected after Hurricane Irma is likely attributed to both direct mortality from the storm and flooding, as well as indirect mortality from the loss of critical, salt-sensitive herbaceous cover. Because climate-change models suggest increases in future flooding and hurricane frequency, we recommend that wildlife managers continue to closely monitor the recovery of LKMR populations and their habitat to determine if more active management actions (e.g., habitat remediation, translocations, or captive breeding) are necessary.