The frequency of high-intensity hurricanes has increased in past decades, making it necessary to understand their impacts on biological diversity. The disturbance by cyclones adds to the anthropic disturbance and generates important effects on ecosystems. Bats are ideal bioindicators that show several responses to impacts of hurricanes in insular systems. However, little is known about their usefulness in assessing impacts of hurricanes in continental regions. We aimed to analyze the short-term impact of Hurricane Patricia (category 4) and anthropic disturbance on the diversity of bats in coastal Jalisco, Mexico, and on abundance of functional groups. We sampled bats at three locations before Hurricane Patricia and eight months after. During a sampling effort of 7091 m2 of netting we captured 487 bats of 17 species, 12 of which were phyllostomids. We detected a decrease in diversity of bats and a more similar composition of species among locations after the hurricane, and a greater stability in species composition and trophic structure in the location with more conserved dry forest. Bats responded in different ways according to functional group. The most vulnerable species were nectarivores, small, with low mobility, and with preferences for understory and cavities. However, their changes in abundance were different among locations and habitats. Conversely, abundance of frugivores-omnivores and insectivores was greater after the hurricane. Additionally, greater changes in abundance among functional groups were in more disturbed sites. Our results indicate that maintaining primary forest and remnants of secondary dry forests is vital to mitigate the effects of major natural disturbances on biodiversity in continental regions.