Closely related species often have remarkably different vocalizations. Some of the variation in acoustic structure may result from species adapting their calls to maximize transmission through their acoustic environments. We document the relative magnitude of inter- and intraspecific variation in acoustic transmission properties of the habitats of three closely related marmot species to study the relative importance that the acoustic environment may have played in selecting for species-specific marmot alarm calls. We used spectrogram correlation to quantify the degree to which pure tones and alarm calls changed as they were broadcast through marmot home ranges to describe the acoustic habitats of golden (M. candata aurea), yellow-bellied (M. flaviventris), and alpine (M. marmota L.) marmots. Species lived in quantifiably different acoustic habitats. One analysis partitioned variation between species and between marmot social groups (nested within species). We found significant interspecific variation in the acoustic transmission fidelity of the three species' habitats and insignificant intraspecific variation between social groups. Further analysis of a larger sample of alarm calls broadcast through golden marmot social groups found significant intraspecific variation. Interspecific variation greater than intraspecific variation suggests that variable acoustic habitats may be responsible for at least some of the interspecific variation in alarm call structure. This is the first study to use spectrogram correlation to describe habitat acoustics. We discuss aspects of the method that may be useful for others seeking to quantify habitat acoustics.