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Background  Babesiosis is an important haemoparasitic disease, caused by the infection and subsequent intra-erythrocytic multiplication of protozoa of the genus  Babesia  that impacts the livestock industry and animal health. The distribution, epidemiology and genetic characterization of  B. bigemina ,  B. bovis , and  B. ovata  in cattle in China as well as the prevalence of these protozoan agents were assessed.    Methods  A total of 646 blood specimens from cattle, dairy cattle and yaks from 14 provinces were collected and tested for the presence of the three  Babesia  species via a specific nested PCR assay based on the  rap-1  and  ama-1  genes. The PCR results were confirmed by DNA sequencing. Gene sequences and the genetic characterization were determined for selected positive samples from each sampling area.    Results  Of a total of 646 samples, 134 (20.7 %), 60 (9.3 %) and 10 (1.5 %) were positive for  B. bovis ,  B. bigemina  and  B. ovata  infections, respectively. Mixed infections were found in 7 of 14 provinces; 43 (6.7 %) samples were infected with  B. bovis  and  B. bigemina . Three samples (0.5 %) exhibited a co-infection with  B. bovis  and  B. ovata , and 6 (0.9 %) were infected with all three parasites. The  rap-1a  gene of  B. bovis  indicated a high degree of sequence heterogeneity compared with other published  rap-1a  sequences worldwide and was 85–100 % identical to  B. bovis rap-1a  sequences in Chinese isolates.  B. bigemina rap-1c  and  B. ovata ama-1  genes were nearly identical, with 97.8–99.3 % and 97.8–99.6 % sequence identity, respectively, in GenBank.    Conclusions  Positive rates of  B. bovis  and  B. bigemina  infection are somewhat high in China. The  B. bovis  infection in yaks was first reported. The significant sequence heterogeneity in different variants of the  rap-1a  gene from Chinese  B. bovis  isolates might be a great threat to the cattle industry if RAP-1a protein is used as immunological antigen against  Babesia  infections in China. The data obtained in this study can be used to plan effective control strategies against babesiosis in China.    Electronic supplementary material  The online version of this article (doi:10.1186/s13071-015-1110-0) contains supplementary material, which is available to authorized users.

Genetic characterization and molecular survey of Babesia bovis, Babesia bigemina and Babesia ovata in cattle, dairy cattle and yaks in China