Population differences in acoustic signals, have been investigated for five decades to better understand the evolution of communication. When receivers are able to discriminate among signals and to react accordingly, geographic differences can have major impacts on the ability of conspecifics to communicate. Surprisingly, population differences in alarm calls and their consequences on the communication process have been so far neglected despite their crucial role on individuals' survival. Working with four wild populations of Alpine marmots (Marmota marmota), we found differences in the acoustic structure of their alarm calls. These differences can neither be explained by geographic, nor genetic distances but rather by other mechanisms including random processes. Moreover, playback experiments provided evidence that receivers discriminate among alarm calls from their own versus other populations, with responses being lower in intensity when the call bout played back originated from their own population. Research on the mechanistic causes of geographical markers and on the relationship between geographical variation, reliability of the signal and behavioural responses are now required to better understand how predation pressure and natural selection could drive the evolution of communication.