AbstractThe genotypes of 10 indigenous Chinese cattle breeds and three introduced breeds were investigated using 10 microsatellite DNA markers recommended by the Food and Agriculture Organization of the United Nations (FAO) and the International Society of Animal Genetics (ISAG) through fluorescence-multiplex PCR. The allele frequency, polymorphism information content (PIC), and heterozygosity were computed to estimate the genetic variation of each population. To determine the genetic relationships among the breeds, phylogenetic trees were constructed based on Nei’s genetic distance and Nei’s standard genetic distance using the unweighted pair-group method with arithmetic mean. As a result, 13 breeds were clustered into three groups. The first group belongs to the common cattle breeds including Yanbian, Changbai, Yanjiang, Monggol, Altay White Head, Hazake, Fuzhou, and Tibetan, while the second group contains those with zebu blood including Xigazê Humped and Apeijiaza. The third group consists of foreign breeds including German Yellow, Simmental, and Charolai. The results may provide a scientific basis for the study of characteristics of Chinese indigenous cattle breeds so as to preserve and utilize them.