Background Several members of genusBabesiaare important pathogens causing babesiosis in dogs. In China, at least fiveBabesiaspecies have been described in dogs or ticks. This study sought to determine the prevalence and molecular characteristics of variousBabesiaspp. in dogs in cities in Shaanxi Province in China, including Xi'an and Hanzhong. Methods A total of 371 blood samples were collected from pet dogs presenting to veterinary clinics in the cities of Xi'an and Hanzhong in Shaanxi, China.Babesiaspp. DNA was detectedviaamplification of partial18SrRNA genes by semi-nested PCR. Almost full-length18SrRNA, ITS, partialTRAPand completecytbgenes were recovered for analysis of the genetic characteristics and relationships with known isolates. Results A single species,Babesia gibsoni, was identified in dogs in Xi'an and Hanzhong. Consistently,B. gibsoniwas also detected in 14 ticks collected from positive dogs. Sequence similarities and phylogenetic analysis suggested that the isolates identified herein showed a closer genetic relationship with isolates from East Asian countries rather than India, Bangladesh, or the USA. Sequence analysis based on tandem repeat analysis of theTRAPgene further revealed that specific haplotypes were circulating in both Xi'an and Hanzhong, with no specific regionality. In addition, 10.9% of all isolates with atovaquone (ATV)-resistance were identified because of M121I mutation in the deduced cytb protein. Conclusions This study revealed a high prevalence rate ofBabesiainfection.Babesia gibsoniwas the onlyBabesiaspecies identified in cases of canine babesiosis in the cities of Xi'an and Hanzhong cities in Shaanxi, China. In addition, theTRAPgene presented high genetic diversity across isolates. Such information is useful for elucidating the epidemiological characteristics of canine babesiosis, as well as the overall genetic diversity ofBabesiaspp. circulating in dog populations in Shaanxi Province.