The aim of the present study was to estimate changes in plant species composition in several forest communities caused by changes in endangered Key deer (Odocoileus virginianus clavium) densities in the National Key Deer Refuge in the lower Florida Keys. Baseline vegetation quadrats from a 1990 study were resampled in 2002 (the present study) in buttonwood transition, hardwood hammock, and mangrove wetland communities (all deer habitat) on 12 islands with low, medium, and high Key deer densities. On islands with high Key deer densities (>17 deer km⁻²), the relative densities of preferred plant species <1.2 m tall significantly decreased over time in each deer habitat, and nonpreferred species <1.2 m tall significantly increased in hammock and mangrove habitats. No significant changes were observed in densities of plant species <1.2 m tall on islands with low and medium Key deer densities (<8 deer km⁻²). Relative densities of preferred plant species >1.2 m tall (midstory/canopy) also significantly decreased in hammock on islands with high deer density, suggesting that heavy browsing is deterring plant growth/recruitment, thus already affecting regeneration of certain plant species into the midstory/canopy tiers. Plant species richness did not vary significantly between 1990 and 2002 for islands with high deer densities, but tended to increase slightly on islands with low deer density in buttonwood and hammock communities. Evidence from this study suggests that high densities of Key deer influence plant species composition on certain islands. We suggest that management plans for Key deer should incorporate both species protection components and population control techniques dependent on deer density-island associations.