Numerous ecological and evolutionary processes are thought to play a role in maintaining the high plant species diversity of tropical forests. An understanding of the phylogenetic structure of an ecological community can provide insights into the relative importance of different processes structuring that community. The objectives of this study were to measure the phylogenetic structure of Neotropical forest tree communities in the Forest Dynamics Plot (FDP) on Barro Colorado Island, Panama, to determine how the phylogenetic structure of tree communities varied among spatial scales and habitats within the FDP, and to study the effects of null-model choice on estimates of community phylogenetic structure. We measured community phylogenetic structure for tree species occurring together in quadrats ranging in size from 10 x 10 m to 100 X 100 m in the FDP. We estimated phylogenetic structure by comparing observed phylogenetic distances among species to the distribution of phylogenetic distances for null communities generated using two different null models. A null model that did not maintain observed species occurrence frequencies tended to find nonrandom community phylogenetic structure, even for random data. Using a null model that maintained observed species frequencies in null communities, the average phylogenetic structure of tree communities in the FDP was close to random at all spatial scales examined, but more quadrats than expected contained species that were phylogenetically clustered or overdispersed, and phylogenetic structure varied among habitats. In young forests and plateau habitats, communities were phylogenetically clustered, meaning that trees were more closely related to their neighbors than expected, while communities in swamp and slope habitats were phylogenetically overdispersed, meaning that trees were more distantly related to their neighbors than expected. Phylogenetic clustering suggests the importance of environmental filtering of phylogenetically conserved traits in young forests and plateau habitats, but the phylogenetic overdispersion observed in other habitats has several possible explanations, including variation in the strength of ecological processes among habitats or the phylogenetic history of niches, traits, and habitat associations. Future studies will need to include information on species traits in order to explain the variation in phylogenetic structure among habitats in tropical forests.