Forested wetlands are in decline, as are many species that are obligate residents. Big Cypress fox squirrels (BCFS; Sciurus niger avicennia) are a threatened endemic to wet pine and cypress forests in southwestern Florida. The region is characterized by development resulting in habitat loss, habitat fragmentation, and hydrological change that influence the quality of these wet forests. Through radiotelemetry and field observations, we examined the ecology and habitat use of BCFS in a natural cypress dome-pine forest mosaic. BCFS selected cypress domes for food and nests throughout the year. Cypress dome habitats were the only habitat type to be used more than available; however, the availability of nearby pine forest was also important. Home ranges were large relative to other tree squirrels, with male home ranges exceeding female ranges. Males overlapped more females than males, while sharing similar food preferences and use patterns with females, suggesting that the sexual dimorphism in home range size is related to mate searching. Roads and oil extraction pads were used less frequently than expected and were incorporated into home ranges less than randomly generated features. The importance of cypress domes within the wet forests and grasslands of Big Cypress National Preserve demonstrates the value of maintaining this delicate mosaic.