Approximately 90% of pine rockland habitat in South Florida and the Florida Keys, USA, has been lost, fragmented, and degraded due to urbanization and other anthropogenic disturbances. Low-lying islands and coastal areas are also becoming increasingly vulnerable to sea-level rise and high tide flooding, which is rapidly increasing in frequency, depth, and extent, putting these areas and the pine rockland habitat they contain at particular risk to these threats. We evaluated changes in habitat under future sea level rise conditions and human development for two species of snakes that are endemic to the pine rocklands, Rim Rock Crowned snake (Tantilla oolitica) and Key Ringneck snake (Diadophis punctatus acrinus), both of which are state-listed endangered species and are under consideration for federal listing. We used recent and historical species records to determine the current extent of available habitat in South Florida. We then predicted: 1) how much (area and percentage) of habitat currently available to these species will be lost due to sea level rise/development, and (2) how does the quality of remaining rockland habitat change in future due to SLR and habitat degradation? We also asked whether threats differ between species and regions. Our results predict that salt water intrusion will negatively affect upland habitat by 2050 with 80% of the existing pine rockland habitat degraded with 42 cm of sea level rise. Moreover, short-term stochastic events, such as storm surge and king tides, will increasingly inundate the root zone of pine and other terrestrial vegetation before complete inundation. Our results further predict that most of the terrestrial habitat used by these species will be underwater by 2080, indicating that sea level rise will likely change current pine rockland habitat into more halophytic habitat (mangrove or salt marsh wetland) in about 50 to 60 years.