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Background: Rodents are recognized as the hosts of many vector-borne bacteria and protozoan parasites and play an important role in their transmission and maintenance. Intensive studies have focused on their infections in vectors, especially in ticks, however, vector-borne bacterial and protozoan infections in rodents are poorly understood although human cases presenting with fever may due to their infection have been found. Methods: From May to October 2019, 192 wild rodents were trapped in wild environment of Guangxi Province, and the spleen samples were collected to reveal the presence of vector-borne bacterial and protozoan infections in them. The microorganisms in rodents were identified by detecting their DNA using (semi-)nested PCR. All the PCR products of the expected size were subjected to sequencing, and then analyzed by BLASTn. Furthermore, all the recovered sequences were subjected to nucleotide identity and phylogenetic analyses. Results: As a result, 192 rodents representing seven species were captured, and Bandicota indica were the dominant species, followed by Rattus andamanensis. Based on the (semi-)nested PCR, our results suggested that Anaplasma bovis, Anaplasma capra, Anaplasma ovis, Anaplasma phagocytophilum, "Candidatus Neoehrlichia mikurensis", "Candidatus E. hainanensis", "Candidatus E. zunyiensis", three uncultured Ehrlichia spp., Bartonella coopersplainsensis, Bartonella tribocorum, Bartonella rattimassiliensis, Bartonella silvatica, two uncultured Bartonella spp., Babesia microti and diverse Hepatozoon were identified in six rodent species. More importantly, six species (including two Anaplasma, two Bartonella, "Ca. N. mikurensis" and Bab. microti) are zoonotic pathogens except Anaplasma bovis and Anaplasma ovis with zoonotic potential. Furthermore, dual infection was observed between different microorganisms, and the most common type of co-infection is between "Ca. N. mikurensis" and other microorganisms. Additionally, potential novel Bartonella species and Hepatozoon species demonstrated the presence of more diverse rodent-associated Bartonella and Hepatozoon. Conclusions: The results in this work indicated great genetic diversity of vector-borne infections in wild rodents, and highlighted the potential risk of human pathogens transmitted from rodents to humans through vectors. Author summary: Rodents are the important hosts of many pathogens, especially vector-borne pathogens, and can harbor and transmit them to humans and cause diseases. In China, little information is known about the infection of vector-borne pathogens in rodents although the rodent species are very diverse. In this study, seven wild rodent species were collected to identify the genetic diversity of vector-borne bacteria and protozoan. Interestingly, diverse vector-borne microorganisms, including four Anaplasma, five Ehrlichia, "Candidatus Neoehrlichia mikurensis", six Bartonella, Babesia microti and diverse Hepatozoon were identified in six rodent species. Furthermore, two potential novel Bartonella species were detected. All these data suggested great genetic diversity of vector-borne pathogens infections in rodents. Of them, six species (including two Anaplasma, two Bartonella, "Ca. N. mikurensis" and Bab. microti) are pathogenic to humans except A. bovis and A. ovis with zoonotic potential, suggesting significant risks to local human population. [ABSTRACT FROM AUTHOR]