1.Gut microbial communities provide many physiological functions to their hosts, especially in herbivorous animals. We still lack an understanding of how these microbial communities are structured across hosts in nature, especially within a given host species. Studies on laboratory mice have demonstrated that host genetics can influence microbial community structure, but that diet can overwhelm these genetic effects. 2.We aimed to test these ideas in a natural system, the American pika (Ochotona princeps). First, pikas are high elevation specialists with significant population structure across various mountain ranges in the USA, allowing us to investigate whether similarities in microbial communities match host genetic differences. Additionally, pikas are herbivorous, with some populations exhibiting remarkable dietary plasticity and consuming high levels of moss, which is exceptionally high in fiber and low in protein. This allows us to investigate adaptations to an herbivorous diet, as well as to the especially challenging diet of moss. 3.Here, we inventoried the microbial communities of pika cecal pellets from various populations using 16S rRNA sequencing to investigate structuring of microbial communities across various populations with different natural diets. 4.Microbial communities varied significantly across populations, and similarities in microbial community structure were congruent with genetic differences in host population structure, a pattern known as 'phylosymbiosis'. 5.Several microbial members (Ruminococcus, Prevotella, Oxalobacter, Coprococcus) were detected across all samples, and thus likely represent a 'core microbiome'. These genera are known to perform a number of services for herbivorous hosts such as fiber fermentation and the degradation of plant defensive compounds, and thus are likely important for herbivory in pikas. Moreoever, populations of pikas that feed on moss harbored microbial communities highly enriched in Melainabacteria. This uncultivable candidate phylum has been proposed to ferment fiber for herbivores, and thus may contribute to the ability of some pika populations to consume high amounts of moss. 6.These findings demonstrate that both host genetics and diet can influence the microbial communities of the American pika. These animals may be novel sources of fiber-degrading microbes. Last, we discuss the implications of population-specific microbial communities for conservation efforts in this species. This article is protected by copyright. All rights reserved.