As there are few studies of Babesia spp. infection in cats in China, or anywhere in the world, the aim of this study was to explore the epidemic features of babesiosis in pet cats in China. In total, 429 blood samples were randomly collected in four different geographical regions. The 18S rRNA gene fragment of Babesia spp. was amplified by nest polymerase chain reaction (PCR), and haplotype and phylogenetic analysis of Babesia were performed to analyze the relationship of this protozoa. The total positive rate of infection was 2.8%. BLAST analysis indicated that Babesia gibsoni was detected in 12 cats. Among these, 4.3%, 3.1%, 0.8% and 2.0% were from Chongqing, Fujian, Hubei and Shandong, respectively. Haplotype and phylogenetic analysis showed that there were nine haplotypes and no obvious genetic variation among B. gibsoni populations. These findings will be helpful for understanding the epidemiology of Babesia spp. in China, and provide a foundation for developing effective preventative strategies.