Habitat refuges are important ecological spatial components that can alter the survivability of organisms by providing relief from ecological pressure, such as predation, disease prevalence, and environmental stressors. If a habitat is considered to be a disease refuge this means that something unique occurred that reduced disease prevalence and intensity. Two different types of oyster habitats (mangroves and reefs) and micro habitats (low and high prop roots and reefs) were studied to determine whether differences in the internal environmental of oysters varied between habitats. Analysis of internal oyster surface and body temperatures along with oyster body salinity showed that differences in microhabitats affected body temperature and salinity. Oysters in both mangrove habitats exhibited lower body salinity and lower temperature than those on oyster reefs. We also analyzed disease prevalence and intensity of Perkinsas marinas among the different habitats and micro habitats by collecting oysters that were >1 year old. Results indicated variability of disease prevalence and intensity among the different habitats, with lowered disease prevalence and intensity seen on mangrove prop roots. These results indicate that mangrove prop roots may provide a habitat refuge for oysters from the parasite Perkinsas marinas.