To understand the influence of hosts, habitats and other factors on the ectoparasites, the clusters of small mammals in different habitat regions in western Yunnan of China and the ectoparasitic gamasid mites on their body surface were studied. The investigated indoor (houses, barns and stables) and outdoor cultivated areas (rice fields, dry tillable lands and bush areas etc.) were divided into two habitats and five regions forming 10 habitat regions (five indoor habitat regions and five outdoor habitat regions) according to the altitude and zoogeographical position. Fuzzy clustering analysis was used to classify the community-groups of the gamasid mites and their small mammal hosts. All the small mammal host communities in 10 habitat regions were clustered into two community groups, indoor group and outdoor group. In each group, the host community in the highest altitude region showed a low similarity to that in other altitude regions. The clustering pattern of gamasid mite communities in different habitat regions did not follow that of the small mammal host communities in the corresponding habitat regions exactly, but all the mite communities in the indoor habitats were still clustered into one group prominently. The results implied that the habitats (indoor and outdoor) may be the most prominent factor influencing the distribution of small mammals and the altitude may come next. Though the distribution of the gamasid mites could be influenced by the habitats and altitude etc., the hosts are considered the most prominent influencing factor.