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Abstract The gut microbiome of animals varies by age, diet, and habitat, and directly influences individual health. Similarly, variation in an individual’s home range can lead to differences in feeding strategies and fitness. Ungulates (hooved mammals) exhibit species-specific microbiomes and habitat use patterns: here, we combined gut microbiome and movement data to assess relationships between space use and the gut microbiome in a specialist and a generalist ungulate. We captured and GPS radiocollared 24 mountain goats ( Oreamnos americanus ) and 34 white-tailed deer ( Odocoileus virginianus ). We collected fecal samples and conducted high-throughput sequencing of the 16S rRNA gene. Using GPS data, we estimated core (50%) and home range (95%) sizes and calculated proportional use for several important habitat types. We generated metrics related to gut diversity and key bacterial ratios. We hypothesize that larger Firmicutes to Bacteroides ratios confer body size or fat advantages that allow for larger home ranges, and that relationships between gut diversity and disproportionate habitat use is stronger in mountain goats due to their restricted niche relative to white-tailed deer. Firmicutes to Bacteroides ratios were positively correlated with core range area in both species. Mountain goats exhibited a negative relationship between gut diversity and use of two key habitat types (treed areas and escape terrain), whereas no relationships were detected in white-tailed deer. This is the first study to relate core range size to the gut microbiome in wild ungulates and is an important proof of concept that advances the information that can be gleaned from non-invasive sampling.