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The dry forests of southern Ecuador are characterized by a great floristic variety and high endemism rates in different taxonomic groups; however, these forests are disappearing at an alarming rate due to anthropogenic disturbances. Epiphytic cryptogams (bryophytes and lichens) are important in seasonally dry tropical forests (SDTFs) and, due to their physiology (poikilohydric species), are sensitive to the changes associated with specific human disturbances. We examined the response of epiphytic cryptogams to habitat disturbance in SDTFs (natural and semi-natural forests) by registering the frequency and coverage of epiphytic cryptogams on 182 trees. We recorded a total of 53 epiphytic cryptogams (47 lichens and 6 bryophytes). A greater number of species was found in the natural forest, with 51 species, than the semi-natural forests (DFs), which had 45 species. We found that total richness tended to decrease with increased intensity of disturbance. The impoverishment was particularly related to the reduction in tree density and diversity (e.g., selective logging) in semi-natural compared to natural forests. However, the epiphytic composition showed little relationship with forests disturbance. We conclude that anthropic disturbance, particularly selective logging, are the main factors affecting the diversity of epiphytic cryptogams in the SDTFs from southern Ecuador.