Background: Ticks are arthropods that can carry multiple pathogens and parasitize on livestock and mammals as well as on humans. Animal husbandry in Inner Mongolia, China, provides a suitable tick habitat. In this study, PacBio full-length 16S rDNA third-generation sequencing was used to analyze the diversity of microbial communities carried by ticks in different regions of Inner Mongolia. The aim of the study is to characterize the microbiome carried by ticks in different geographical locations and to provide theoretical support for regional prevention and control of pathogen populations in the future. Methods: In this study, a total of 905 Dermacentor nuttalli and 36 Ixodes persuleatus were collected from the surface of sheep in four main pasture areas in Inner Mongolia. Pooled DNA samples were prepared from three samples from each region and from each tick species. In total the microbial diversity of 12 samples was analyzed by PacBio full-length 16S rRNA third-generation sequencing, and the α and β diversity were determined. Results: The main bacterial genera we found were Rickettsia (35.27%), Ac37b (19.33%), Arsenophonus (11.21%), Candidatus Lariskella (10.84%), and Acinetobacter (7.17%). There were significant differences in the microbial composition of ticks from different regions and in different tick species. Rickettsia bellii was found in the I. persuleatus group. In addition, Anaplasma and a novel tyhpus group Rickettsia species (R. bacterium Ac37b) were found in the sample group of D. nuttalli in the city of Ordos.Conclusions: In this study, Rickettsia bellii was first found in I. persuleatus in Inner Mongolia, and a novel tyhpus group Rickettsia species (R. bacterium Ac37b) was found in D. nuttalli from the city of Ordos. Our study provides a basis for the prevention and control of tick-borne diseases through the analysis of tick microbial diversity in different regions of Inner Mongolia. Furthermore, we were able to detect a new tick-borne pathogen in D. nutalli.