We sampled fish communities in 19 isolated cypress pond and herbaceous marsh wetlands at locations in southwest, south-central, and southeast Florida. Breder fish traps were more effective at sampling fish communities at these sites than either seine or dip nets. We collected 23 total species, but species richness varied from 1–16 among sites. The availability of deepwater refugia and the extent to which periodic flooding connected these wetland habitats to other aquatic environments appeared to be principal factors influencing composition of fish assemblages. Models of fish distribution in response to hydrological changes in the Everglades have proposed size-structured, fish functional groups of ≤ or > 7 cm, but our data suggested size and ecology of fish functional groups in isolated wetlands may be better described as small, omnivorous species (≤15 cm) and larger predatory species (> 15 cm). We suggest incorporating fish functional groups in programs to monitor ecological health of isolated wetlands in south Florida may be more productive than attempts to identify specific indicator species or relying solely upon measurements of physical, chemical, or plant-community parameters.