Little is known about non-mycorrhizal endophytic fungi in tropical orchids; still less is known about how endophytes vary within and between individual orchid plants. Fungal endophytes were isolated from roots and leaves of epiphytic and lithophytic orchids in the genus Lepanthes; seven species, from rainforests in Puerto Rico, were sampled. The endophytes observed most frequently were Xylaria species and Rhizoctonia-like fungi, found in 29% of roots and 19% of leaves, and 45% of roots and 31% of leaves, respectively. Five deuteromycete genera were also isolated, occurring in 19% of roots and 43% of leaves (combined). At least nine species of Xylaria were found, with several species sometimes occurring in a single plant. Differences between roots and leaves in frequency of Xylaria and Rhizoctonia isolates were not significant, although differences among orchid species in number and types of endophytes were. Heterogeneity of endophytes in single plants and plant organs was greater than differences between species. Many Lepanthes species are very restricted in distribution, and knowledge of their interactions with endophytes might be useful in species management.