In this study, we carried out an inventory of butterfly diversity and an analysis of alpha and beta diversity considering the effects of phenology and degree of disturbance in tropical dry forest. The study included three localities: Cañadas de Ajuchitlán and El Limón, situated within the Sierra de Huautla Biosphere Reserve (REBIOSH) natural protected area, and San Miguel de los Elotes, which is outside of the REBIOSH. We systematically sampled each of the localities using two collection methods once per month for a full year (April 2013 to March 2014). A total of 4,017 specimens belonging to 119 species and 83 genera were collected. We recorded for the first time the presence of Perichares aurina Evans (Lepidoptera, Hesperiidae), in Mexico, 14 additional Hesperiidae species were new records for Morelos, Mexico, and 16% of the species recorded in this study are endemic to Mexico. Species richness was highest in August for the two localities (Cañadas de Ajuchitlán and El Limón), located within the REBIOSH. Species richness was highest in November for San Miguel de los Elotes, which is outside of the REBIOSH. In terms of the alpha diversity values (⁰D, observed diversity), Cañadas de Ajuchitlán had the highest species richness. In the analysis of similarity (Beta diversity), the two localities within the REBIOSH had the highest species similarity, despite being the most geographically distant.