Variation in the acoustic structure of bat echolocation calls can often provide sufficient information for reliable and efficient species identification. The aim of this study was to investigate the use of echolocation call structure to identify a number of bats in the families Vespertilionidae, Emballonuridae, Nycteridae and Megadermatidae from Thailand. These species typically emit echolocation calls with a frequency-modulated (FM) sweep dominating part or all of their calls. A total of 510 echolocation calls from free-flying individuals were recorded throughout Thailand. According to the frequency-time spectra, these calls were categorized into four types: broadband FM (eight species), narrowband FM (seven species), long multiharmonic (four species) and short multiharmonic (three species). Discriminant function analysis was used to classify calls from individual bats to species. Correct classification levels were 85.9% for individuals emitting broadband FM calls (six species with adequate sample sizes), 70.4% for narrowband FM bats (seven species), 84.4% for species emitting long multiharmonic calls (four species) and 96.7% for species emitting short multiharmonic calls (two species with adequate sample sizes). However, classification rates were often low at the species level. Acoustic identification of bats emitting FM calls should be approached with caution in species-rich communities, in contrast with the identification of rhinolophoid bats where many species use distinctive constant frequencies that can facilitate identification, and provides a basis for rapid acoustic surveys of large areas in Thailand, and potentially other parts of Southeast Asia.