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Bats serve as natural hosts for various infectious agents that can affect both humans and animals, and they are geographically widespread. In recent years, the prevalence of bat-associated pathogens has surged on a global scale, consequently generating significant interest in bats and their ectoparasites. In this study, we specifically selected the Miniopterus fuliginosus as the host and conducted bat captures in Nanjian Yi Autonomous County, Dali Bai Autonomous Prefecture, and the other in Mouding Township, Chuxiong Yi Autonomous Prefecture, located in Yunnan Province, China. Ectoparasites were meticulously collected from the bat body surface, alongside blood samples for subsequent analyses. Following collection, the ectoparasites were methodically identified and subjected to comprehensive ecological analysis. Additionally, DNA was extracted from both the bat blood and bat flies, with conventional PCR techniques utilized for molecular screening of four pathogens: Anaplasma sp., Babesia sp., Hepatozoon sp., and Bartonella sp. The capture efforts yielded a total of 37 M. fuliginosus , from which 388 ectoparasites were recovered, including 197 gamasid mites (C r = 50.77%, P M = 94.59%, M A = 5.32, M I = 5.63) and 191 bat flies (C r = 49.23%, P M = 75.68%, M A = 5.16, M I = 6.82). Notably, Steatonyssus nyctali (Y = 0.28, m*/m = 2.44) and Nycteribia allotopa (Y = 0.23, m*/m = 1.54) predominated among different individuals of M. fuliginosus , exhibiting an aggregated distribution pattern. The infection rates of Bartonella sp. were identified to be 18.92% (7/37) among bats and 37.17% (71/191) among bat flies, based on the testing of 37 bats and 191 bat flies. Phylogenetic analysis demonstrated that the Bartonella sequences exhibited similarity to those found in bats and bat flies within China and South Korea. This study not only contributes to our comprehension of ectoparasite infection in M. fuliginosus but also establishes a foundation for potential exploration of their role as vectors. [Display omitted] • Ecological analysis of ectoparasites on bats collected from Yunnan, China. • Investigating the presence of four pathogens carried by bats and their ectoparasites. • Providing reference for the vector potential of ectoparasites on bats. [ABSTRACT FROM AUTHOR]