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Bats can harbor zoonotic pathogens causing emerging infectious diseases, but their status as hosts for bacteria is limited. We aimed to investigate the distribution, prevalence and genetic diversity of Borrelia in bats and bat ticks in Hubei Province, China, which will give us a better understanding of the risk of Borrelia infection posed by bats and their ticks. During 2018–2020, 403 bats were captured from caves in Hubei Province, China, 2 bats were PCR-positive for Borrelia. Sequence analysis of rrs, flaB and glpQ genes of positive samples showed 99.55%-100% similarity to Candidatus Borrelia fainii, a novel human-pathogenic relapsing fever Borrelia species recently reported in Zambia, Africa and Eastern China, which was clustered together with relapsing fever Borrelia species traditionally reported only in the New World. Multilocus sequence typing (MLST) and pairwise genetic distances further confirmed the Borrelia species in the bats from Central China as Candidatus Borrelia fainii. No Borrelia DNA was detected in ticks collected from bats. The detection of this human-pathogenic relapsing fever Borrelia in bats suggests a wide distribution of this novel relapsing fever Borrelia species in China, which may pose a threat to public health in China. Author summary: Bats have a wide range of species and distribution, these mammals have been proposed as the natural reservoirs of pathogens for many years. Previous research focus mainly on viral agents in bats, while the infection of Borrelia spirochetes in bats is much neglected. Borrelia species causing Lyme disease and relapsing fever have been found in a wide range of ticks. Relapsing fever has long been recognized as major cause of disease and death in Africa, but as more and more cases reported in different continents, relapsing fever has become an emergent disease. There is growing evidence that bats can play a role in carrying Borrelia species. In this study, we captured different species of bats from caves during 2018–2020 in Central China, tested liver tissue for Borrelia by PCR, and applied multilocus sequence typing (MLST) to identify this bacterium. Our study found human pathogenic relapsing fever Candidatus Borrelia fainii in Central China, suggesting bat borne Borrelia spirochetes may pose a threat to public health in China. [ABSTRACT FROM AUTHOR]