[Background]China has a great diversity of ecosystems and an abundance of cattle resources,with nearly 30 million indigenous cattle of 53 indigenous cattle breeds.Traditionally, Chinese indigenous breeds were classified morphologically and phylogenetically into two groups, humped (zebu or A. indicine) and humpless (E. taurine). In this study, a total of 558 samples from 17 indigenous breeds and 3 improved breeds, were analyzed to explore the genetic variation and population structure of Chinese indigenous breeds.