Knowledge about the factors shaping the rumen microbiota in wild animals is limited. Therefore, the aim of this study was to compare the microbiota from the three cervid species moose (Alces alces, n = 5), red deer (Cervus elaphus, n = 4) and roe deer (Capreolus capreolus, n = 12), sharing the same habitat. Using deep 16S rRNA gene sequencing, we found that the largest species moose had the highest number of unique operational taxonomic units. Furthermore, red deer and moose shared more of the microbiota, compared with the smallest species, roe deer, with Firmicutes and Euryarchaeota being significantly overrepresented for the shared microbiota. These differences could not be explained by diet or range. The animals largely shared the same range, and there are no systematic differences in diet. We therefore believe rumen physiology can be one of the main contributing factors to the observed distribution of the rumen microbiota in cervid species.