Disturbance plays a key role in shaping forest composition and diversity. We used a community phylogeny and long-term forest dynamics data to investigate biotic and abiotic factors shaping tropical forest regeneration following both human and natural disturbance. Specifically, we examined shifts in seedling phylogenetic and functional (i.e., seed mass) community structure over a decade following a major hurricane in a human-impacted forest in Puerto Rico. Phylogenetic relatedness of the seedling community decreased in the first five years post-hurricane and then increased, largely driven by changes in the abundance of a common palm species. Functional structure (based on seed mass) became increasingly clustered through time, due to canopy closure causing small-seeded, light-demanding species to decline in abundance. Seedling neighbor density and phylogenetic relatedness negatively affected seedling survival, which likely acted to reduce phylogenetic relatedness within seedling plots. Across the study site, areas impacted in the past by high-intensity land use had lower or similar phylogenetic relatedness of seedling communities than low-intensity past land use areas, reflecting interactive effects of human and natural disturbance. Our study demonstrates how phylogenetic and functional information offer insights into the role of biotic and abiotic factors structuring forest recovery following disturbance.