The purpose of this study was to investigate tick species around Mount Fanjing and analyze bacterial communities in two species –Rhipicephalus microplusandHaemaphysalis longicornis– parasitizing cattle in Tongren, Guizhou province, Southwest China, using high-throughput sequencing methods. In April 2019, ticks were collected from five sites in Jiangkou County, Yinjiang County, and Songtao County. In total, 296 ticks were collected, comprising two genera and three species:H. longicornis,Haemaphysalis flava, andR. microplus.Rhipicephalus micropluswas the most representative species (57.4%) within the collected group, being the dominant species in Tongren City, followed byH.longicornis(39.5%) andH. flava(3.0%). Beta-diversity analysis revealed differences in bacterial community composition among the tick species. The bacterial community structure ofR.micropluscollected in the three counties was highly similar.ChlorellaandBacilluswere highly abundant inH.longicornis.Rickettsiawas detected at high relative abundance inR.microplusbut in low relative abundance inH.longicornis, suggesting thatRickettsiais more associated withR.microplusthan withH.longicornis. More in-depth investigations are needed to determine the pathogenic risk ofRickettsiaand its relationship with the host. This is the first survey on tick-borne bacterial communities in this area, which is of great significance for the prevention and control of tick-borne diseases locally.Supplementary InformationThe online version contains supplementary material available at 10.1007/s10493-023-00799-y.