1. The gut microbiota of rodents is essential for survival and adaptation, and has been shown to be susceptible to a variety of factors, ranging from environmental conditions to genetic predispositions. Nevertheless, few comparative studies have considered the contribution of species identity and geographic spatial distance to the variation in gut microbiota. 2. Here, we investigated the gut microbial communities of four wild rodent species (Rattus norvegicus, Apodemus agrarius, Cricetulus barabensis, and Tscherskia triton) at five sites in northern China’s farming-pastoral transition zone. By performing a cross-factorial comparison, we are able to test whether belonging to the same species, or instead, being in the same capture site dominates in determining gut microbiota composition. 3. Our analysis found that the Amplicon Sequence Variants (ASVs) showed a partial overlap with the species identity and the geographic capture sites, which did not reveal a ‘phylosymbiosis’ pattern. 4. The gut microbiota of these four rodent species adhered to typical mammalian characteristics, predominantly characterised by the Firmicutes and Bacteroidetes phyla. As the geographic distance between populations increased, the shared microbial taxa among conspecific populations decreased. We observed that within a relatively small geographical range, even different species exhibit convergent α-diversity due to their inhabitation within the same environmental microbial pool. In contrast, the composition and structure of the intestinal microbiota in allopatric populations of A. agrarius showed marked differences, as well as C. barabensis. Additionally, geographical environmental elements, exhibited significant correlations with diversity indices. Conversely, host-related factors had minimal influence on microbial abundance. 5. These findings illuminated that the similarity of the microbial compositions was not determined primarily by the host species, the location of the sampling explained a greater amount of variation in the microbial composition, indicating that the local environment played a crucial role in shaping the microbial composition.