Gamasid mites (Acari: Mesostigmata) are ecologically diverse arthropods, many of which act as vectors for zoonotic diseases such as rickettsial pox and hemorrhagic fever with renal syndrome. This study investigates the faunal and ecological patterns of gamasid mites across five zoogeographic microregions in Yunnan Province, China, a biodiversity hotspot with complex topography. From 1990 to 2022, 18,063 small mammal hosts (primarily rodents) were surveyed, yielding 167 mite species (141,501 specimens). The key findings include the following: (1) Low host specificity: most mite species parasitized >10 host species, with Laelaps nuttalli, L. echidninus, Dipolaelaps anourosorecis, L. guizhouensis, L. turkestanicus, and L. chini dominating (>76.59% abundance). (2) Environmental heterogeneity: mountainous and outdoor habitats exhibited higher mite diversity than flatland/indoor environments. (3) Zoonotic risks: thirteen vector species with low host specificity were identified, potentially amplifying disease transmission. (4) Ecological niche dynamics: high niche overlaps (e.g., Laelaps guizhouensis vs. L. xingyiensis: O-ik = 0.997) and positive interspecific correlations (e.g., L. echidninus vs. L. nuttalli: R = 0.97, p < 0.01) suggest co-occurrence trends on shared hosts. (5) Biogeographic patterns: mite communities were clustered distinctly by microregion, with the highest similarity being obtained between western/southern plateaus (IV and V) and unique diversity in the Hengduan Mountains (I). (6) Chao 1 estimation predicted 203 total mite species in Yunnan, 36 of which were undetected in the current sampling. These results highlight the interplay of biogeography, host ecology, and environmental factors in shaping mite distributions, with implications for zoonotic disease surveillance in biodiverse regions.