The complete D-loop region of mitochondrial DNA from 206 individuals in 16 Chinese indigenous cattle breeds was sequenced and analyzed to detect variability of D-loop region of mitochondria DNA for those breeds. The re-sults showed as follows: 101 variations and 99 haplotypes were found, in which 73 haplotypes were of Bos taurus and the other 26 haplotypes were of Bos indicus, and the average number of nucleotide differences was 22.6920, haplotype diversity was 0.9320, and nucleotide diversity was 0.0227, indicating high genetic diversity in Chinese indigenous cattle breeds. Ac-cording to the NJ phylogenetic tree, 16 cattle breeds were divided into two clades, Bos taurus and Bos indicus. Based on the Network graphics, the 73 haplotypes of Bos taurus were classified into 3 groups and the 26 haplotypes of Bos indicus were classified into 5 groups. It was inferred that cattle breeds of Bos indicus in China had experienced at least 4 population ex-pansions during their movement. There was only 16% of H3 haplotype sequnences similar to the sequence of Nellore, and 84% of those sequnences had purine C variation in Chinese indigenous cattle breeds through the analysis on their common H3 haplotypes. It was concluded that those purine C decrease was possibly originated in Chinese Bos indicus.