The gut microbiota plays a crucial role in the health and well-being of wildlife. However, its composition and diversity remain unexplored, particularly in threatened species such as the Siberian musk deer (SMD). This study aimed to elucidate the gut microbiota composition within different wild SMD communities for assessing their health status. We conducted the first comprehensive fecal microbiome analysis of wild SMD inhabiting three distinct locations in Gangwon Province, Republic of Korea (Korea). Fecal samples were collected non-invasively and 16S rRNA gene sequencing was performed for gut microbiota characterization. Consistent with previous research, Firmicutes and Bacteroidetes were the dominant phyla in the gut microbiota of wild SMD. Planctomycetota was a prevalent phylum in wild SMD gut microbiota, warranting further investigation of its ecological significance. While significant differences were observed in the gut microbiota richness among the three groups, no significant disparities were detected in the beta diversity. Additionally, certain genera exhibited distinct relative abundances among the groups, suggesting potential associations with geographic factors, gut disorders, and dietary habits. Our findings provide valuable insights into the gut microbiome of wild SMD and offer a foundation for future microbiome-based conservation efforts for this vulnerable species.