The flatwoods salamander (Ambystoma cingulatum) was listed as federally threatened in 1999. Alteration of habitat was considered the main threat to the species, especially the loss of habitat for larval flatwoods salamanders that develop in isolated, seasonally flooded wetlands. Our objectives were to evaluate a suite of within-pool factors (i.e., vegetation structure, water level, and an index to presence of fish) that could influence occupancy of breeding wetlands by larval flatwoods salamanders on Eglin Air Force Base in Florida, USA. We dip-netted for larval salamanders from January through March 2003–2006 and we measured a suite of vegetation characteristics in 2006–2007. Further, in 2006 we measured the level of water and relative presence of fish over the salamander breeding season. Site occupancy over the four year period was best described by a model that incorporated high herbaceous vegetation cover and open canopy cover. Detection probability was assessed, but it varied among years and was not included in the model. Our study suggests that managing the breeding habitat of flatwoods salamander for open canopies and dense herbaceous vegetation may contribute to this species' recovery.