We assessed the diversity, vertical distribution, and the effect of structural and geographical factors on the diversity of vascular epiphyte assemblages (VEAs) in two forest types in the “El Cielo” Biosphere Reserve. We found 2839 epiphyte individuals from 15 species on 240 host trees (27 species) in the semideciduous forest and 5085 individuals from 8 species on 215 host trees (12 species) in the pine–oak forest. Epiphytes showed a preference for the middle zone of the host trees. The diversity of VEAs was uneven in both forest types, although the VEA in the semideciduous forest was the most diverse. VEAs across forests were slightly similar in their composition (30% mean overlap), but very different in their structure (i.e., they did not share very abundant species). The variation in species richness among VEAs was influenced by forest structure, independently of forest type. Compositional differences of VEAs among forest types were explained by geographic distance and host-tree identity (31% and 28% variation explained, respectively). By characterizing the diversity of VEAs we provide a basic understanding of the factors influencing epiphyte diversity in these understudied ecosystems.