Due to the close relationships that bats establish with their environments, they have been considered ideal bioindicators for natural ecosystems’ disturbance. We analyzed the species composition of aerial insectivorous bats, using echolocation calls, in gaps and inside tropical rainforests, in order to analyze the influence of these natural disturbances. During May 2009, we evaluated the presence of bats using a frequency division ultrasonic recording device. We found significant differences in species composition between the inside of the forest and gaps (Jaccard= 0.308), and a high variation throughout the forests sites, and high similarities between the forest gaps. We discuss the potential effect of forest gaps in the insectivorous bats’ composition and habitat use, as well as the effect of the sampling method.