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We examined the relationship between habitat structure and alarm call characteristics in six colonies of Gunnison’s prairie dogs (Cynomys gunnisoni) near Flagstaff, Arizona, before and after a mid-summer vegetation change. We found significant differences in alarm call characteristics between colonies, confirming the existence of alarm call dialects. Differences in frequency components but not temporal components of calls were associated with differences in habitat structure. Playback experiments revealed that differences in alarm call structure affected acoustic transmission of calls through the local habitat. Thus, we identify habitat structure as one factor that may contribute to alarm call differences between colonies of Gunnison’s prairie dogs. Relationships between call characteristics and habitat structure changed over seasons. Playback experiments suggested that this changing relationship could reflect a change in the purpose of the alarm call between early and late summer. Some components of alarm calls seem tailored for attenuation over short distances in the early summer but for long-distance transmission at summer’s end. These differences might arise because pups stay close to their natal burrows in the early summer and disperse throughout a colony in late summer. Alternatively, these differences in alarm call transmission between seasons could be caused by the increase in vegetation in the mid-summer. At the end of the summer prairie dogs could be more dependent on long-distance antipredator calls to offset the loss of visibility caused by the increase in vegetation in the late summer