Endophytes are microorganisms that live inside plant tissues without causing symptoms of disease. They are a largely unexplored component of biodiversity, especially in the tropics. In this study, leaves from two populations of Guarea guidonia trees (Meliaceae) in the Luquillo region, Puerto Rico, were screened for diversity and composition of endophytic fungal communities. A total of 268 leaf fragments from 14 trees were surveyed. Thirty-eight morphospecies of endophytes were found. Phomopsis, Colletotrichum, Xylaria, and Rhizoctonia-like fungi were the most abundant taxa. Over 95 percent of the leaf pieces had endophytes. Communities had a few abundant species and many species with few individuals. The fungal community from the Guarea population in a forest preserve was more diverse than that from a disturbed area. Fungal communities were stratified according to height within a tree, but no differences were found between blade, petiolule, and rachis. The data suggest that the smaller and the more scattered the plant fragments sampled, the higher the probability of approaching real diversity values of endophytic fungal communities.