Background: Borrelia miyamotoi is a newly described relapsing fever spirochete transmitted by Ixodid tick species. Little is known about the prevalence of B. miyamotoi infections in humans and ticks in Inner Mongolia, China. Therefore, we investigated the prevalence of B. miyamotoi in Ixodes persulcatus, and we aimed to isolate B. miyamotoi from I. persulcatus ticks from four regions of Greater Hinggan, Inner Mongolia, China.Methods: During May to June of 2016-2019, host-seeking adult ticks of I. persulcatus were collected from vegetation. Genomic DNA was prepared from half of each tick body for PCR template, and the remaining half was used to cultivate B. miyamotoi in BSK-M medium. We employed quantitative real-time PCR (qPCR) to detect Borrelia DNA in the ticks and to calculate the prevalence of B. miyamotoi and other borreliae infections. For the characterization of isolated B. miyamotoi, we performed draft genome sequencing and multi-loci sequencing analysis (MLSA). Results: A total of 2,656 I. persulcatus adult ticks were collected. The over-all prevalence of relapsing fever (RF) borreliae in ticks was 5.0% (134/2,656) and that of Lyme disease (LD) borreliae was 43.8% (1,164/2,656). Co-infection by RF and LD borreliae was observed in 63 ticks (2.4%). Ticks that were positive for RF borreliae on qPCR were subjected to glycerophosphodiester diester phosphodiesterase gene (glpQ) PCR amplification and sequencing, through which we identified the RF borreliae specimens as B. miyamotoi. In this study, we successfully isolated the B. miyamotoi strain Hetao-1 from I. persulcatus, and a draft genome sequence was obtained for the isolate. Genomic sequencing revealed the strain Hetao-1 genome to be approximately 906.1 kbp in length (28.9% average GC content), and MLSA analysis identified the strain as ST633, which was previously reported in Japan and Mongolia.Conclusion: We detected B. miyamotoi from I. persulcatus ticks collected in Inner Mongolia, and successfully isolated a B. miyamotoi strain. To our knowledge, this is the first study to culture a B. miyamotoi isolate in China. The data on the prevalence of B. miyamotoi and other borreliae in I. persulcatus ticks will be fundamental for future epidemiological studies of B. miyamotoi disease in Inner Mongolia.