Abstract：We analysised the genetic diversity and phylogenesis of 225 individuals of 9 sheep populations using mitochondrial D-loop sequences and microsatellite DNA. The results of the two methods in genetic diversity analysis were consistent. It was that Qinghai Tibetan sheep had rich genetic diversity, but Hu sheep and Minxian Black Fur sheep's genetic diversity were lower than others. While in phylogenesis analysis, phylogenetic trees based on mtDNA D-loop sequence and microsatellite DNA were different. Because microsatellite DNA accords with Mendelian inheritance and can reflect population relationship more reliability. mtDNA is extranuclear inheritance and belongs to maternal inheritance and is not superiority in population relationship analysis. Furthermore, the breeding background of Qinghai Merino and Gansu Alpine Merino showed that they had close relationship. This was accorded with phylogenetic tree constructed by microsatellite DNA. Thus we conclude that microsatellite DNA is more reliable in population relationship analysis. Further network analysis of the phylogenetic relationship of the 172 haplotypes identified from 9 sheep populations supported there are three distinct maternal lineages.
