AbstractSeveral studies have investigated the gut bacterial composition of wild ungulates in the Qinghai–Xizang Plateau. However, the relationship between their gut microbiome dendrograms and their phylogenetic tree remains unclear. In this study, we analyzed 45 amplicons (V3–V4 region of the 16S rRNA gene) from five wild ungulates—Pseudois nayaur, Pantholops hodgsonii, Gazella subgutturosa, Bos grunniens, and Equus kiang—from the Qinghai–Xizang Plateau to clarify the relationship between their phylogenies and gut microbiome dendrograms. The unweighted pair group method with arithmetic mean analysis and hierarchical clustering analysis indicated that G. subgutturosa is closely related to P. nayaur; however, these results were inconsistent with their phylogenetic trees. Additionally, the indicator genera in the microbiome of each wild ungulate showed strong associations with the diets and habitats of their host. Thus, diet and space niche differentiation may primarily account for the differences between the gut microbiome characteristics of these wild ungulates and their phylogeny. In summary, our research provides insights into the evolutionary factors influencing the gut microbiome of wild ungulates in the Qinghai–Xizang Plateau.