Deforestation is the most important cause of biodiversity loss in tropical ecosystems. Epiphytic species, lichens and bryophytes, are very sensitive to environmental changes, including those produced by conversion of primary forests into secondary vegetation. However, little is known about the differences between different secondary forests and plantations regarding the epiphytic biota. We compared epiphytic communities among different secondary forests and non-native plantations in southern Ecuador. Four forest typeswere considered: non-native Pinus patula plantations, monospecific secondary forests of Alnus acuminata, monospecific secondary forests of Andesanthus lepidotus and mixed secondary forests. Within each forest type, two stands were surveyed, establishing a total of 80 plots and analyzing four trees per plot. We estimated lichen and bryophyte cover in four inventories per tree and calculated and compared different metrics for taxonomic and functional diversity, as well as community composition. The results revealed forest type as the major predictor for the species and functional traits richness, and for diversity and composition. In total, 422 taxa were identified (312 lichens and 110 bryophytes), with mixed secondary forests having the richest communities (194 species) and nonnative plantations having the lowest richness (105 species). Bryophyte richness was highest in A. lepidotus forests. Taxonomic and functional diversity, and species composition differed greatly among forest types and followed a different pattern depending on the organism considered. Lichens were the most sensitive indicators of environmental conditions associated with different tropical forest types.