Bats emit echolocation calls to orientate in their predominantly dark environment. Recording of species‐specific calls can facilitate species identification, especially when mist netting is not feasible. However, some taxa, such as Myotis bats can be hard to distinguish acoustically. In crowded situations where calls of many individuals overlap, the subtle differences between species are additionally attenuated. Here, we sought to noninvasively study the phenology of Myotis bats during autumn swarming at a prominent hibernaculum. To do so, we recorded sequences of overlapping echolocation calls (N = 564) during nights of high swarming activity and extracted spectral parameters (peak frequency, start frequency, spectral centroid) and linear frequency cepstral coefficients (LFCCs), which additionally encompass the timbre (vocal “color”) of calls. We used this parameter combination in a stepwise discriminant function analysis (DFA) to classify the call sequences to species level. A set of previously identified call sequences of single flying Myotis daubentonii and Myotis nattereri, the most common species at our study site, functioned as a training set for the DFA. 90.2% of the call sequences could be assigned to either M. daubentonii or M. nattereri, indicating the predominantly swarming species at the time of recording. We verified our results by correctly classifying the second set of previously identified call sequences with an accuracy of 100%. In addition, our acoustic species classification corresponds well to the existing knowledge on swarming phenology at the hibernaculum. Moreover, we successfully classified call sequences from a different hibernaculum to species level and verified our classification results by capturing swarming bats while we recorded them. Our findings provide a proof of concept for a new noninvasive acoustic monitoring technique that analyses “swarming soundscapes” by combining classical acoustic parameters and LFCCs, instead of analyzing single calls. Our approach for species identification is especially beneficial in situations with multiple calling individuals, such as autumn swarming.