(1) Background: As a species of gamasid mite, the tropical rat mite (Ornithonyssus bacoti) is a common ectoparasite on rodents and some other small mammals. Besides stinging humans to cause dermatitis, O. bacoti can be a vector of rickettsia pox and a potential vector of hemorrhagic fever with renal syndrome (HFRS). (2) Objective: The present study was conducted to understand the host selection of O. bacoti on different animal hosts and the distribution in different environmental gradients in Yunnan Province of Southwest China. (3) Methods: The original data came from the investigations in 39 counties of Yunnan, between 1990 and 2015. The animal hosts, rodents and some other small mammals were mainly trapped with mouse traps. The O. bacoti mites on the body surface of animal hosts were collected and identified in a conventional way. The constituent ratio (Cr), prevalence (P_M), mean abundance (MA) and mean intensity (MI) were used to reflect infestations of animal hosts with O. bacoti mites. The patchiness index and Taylor's power law were used to measure the spatial distribution pattern of O. bacoti mites on their hosts. (4) Results: A total of 4121 tropical rat mites (O. bacoti) were identified from 15 species and 14,739 individuals of hosts, and 99.20% of them were found on rodents. More than half of O. bacoti mites (51.78%) were identified from the Asian house rat (Rattus tanezumi), and 40.09% of the mites from the Norway rat (R. norvegicus) (p < 0.05). The infestations of R. tanezumi (P_M = 7.61%, MA = 0.40 and MI = 5.31) and R. norvegicus (P_M = 10.98, MA = 1.14 and MI = 10.39) with O. bacoti mites were significantly higher than those of other host species (p < 0.05). The infestations of two dominant rat hosts (R. tanezumi and R. norvegicus) with O. bacoti mites varied in different environmental gradients (latitudes, longitudes, altitudes, landscapes and habitats) and on different sexes and ages of the hosts. The prevalence of juvenile R. norvegicus rats with O. bacoti mites (P_M = 12.90%) was significantly higher than that of adult rats (P_M = 9.62%) (p < 0.05). The prevalence (P_M = 38.46%) and mean abundance (MA = 2.28 mites/host) of R. tanezumi rats with O. bacoti mites in the high latitude were higher than those in the low latitudes (p < 0.05). The majority of the total collected 4121 O. bacoti mites was found in the flatland landscape (91.28%) and indoor habitat (73.48%) (p < 0.05). The P_M (10.66%) and MA (0.49 mites/host) of R. tanezumi rats with O. bacoti mites were significantly higher in the indoor habitat than in the outdoor habitat (p < 0.05). The tropical rat mites showed an aggregated distribution pattern on their first dominant host, R. tanezumi. Conclusion: The tropical rat mite (O. bacoti) is a widely distributed species of gamasid mite in Yunnan Province, Southwest China, and its dominant hosts are two synanthropic species of rats, R. tanezumi and R. norvegicus. It is mainly distributed in the flatland landscape and indoor habitat. It has some host-specificity, with a preference to rodents, especially R. tanezumi and R. norvegicus. The O. bacoti mites are of aggregated distribution on R. tanezumi rats.

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