Bartonellaare generally recognized as zoonotic pathogens of mammals, including many rodent species. However, data on the genetic diversity ofBartonellain some regions are still absent in China. In this study, we collected rodent samples (Meriones unguiculatus,Spermophilus dauricus,Eolagurus luteus, andCricetulus barabensis) from Inner Mongolia located in Northern China. TheBartonellawere detected and identified by sequencing thegltA,ftsZ, ITS, andgroELgenes in them. An overall 47.27% (52/110) positive rate was observed. This may be the first report thatM.unguiculatusandE.luteusharborBartonella. Phylogenetic and genetic analysis ongltA,ftsZ, ITS, andgroELgenes indicated that the strains were divided into seven distinct clades, suggesting the diverse genetic genotypes ofBartonellaspecies in this area. Of those, Clade 5 meets the criteria for identification as a novel species based on gene sequence dissimilarity to knownBartonellaspecies and herein we name it “CandidatusBartonella mongolica”.