Plant rarity is considered a useful predictor of the extinction risk of species. However, apparent rarity can emerge from incomplete data sets or incorrect sampling. Epiphyllous bryophytes are a poorly collected and taxonomically complicated group, with incompletely known distribution patterns. In this paper we explore the diversity patterns and meso- and micro-habitat specialization of common and rare epiphyllous bryophyte species, and evaluate the threat status of Aphanolejeunea gracilis, Leptolejeunea tridentata, and Otolejeunea schnellii. Epiphylls were collected from 240 samples (10 ×10 cm) in 30 plots of 5 ×5 m in superhumid lowland forest of the Chocó, Colombia. Our results indicate that epiphyll diversity and species composition is similar among palm and non-palm leaves. Disturbance had a negative effect on epiphyll cover, species richness, and diversity of rare species. Data on rare species did not correlate with global or national red lists, indicating that detailed surveys are necessary to accurately assess the threat status of “rare” species.