Chionanthus retusus is one of the well-known ornamental trees in East Asia and America. Not only its value in the market but also had the potential as a source for producing antioxidant. However, due to uncontrolled exploitation, the number of wild C. retusus in China is decreasing rapidly. The genetic study of C. retusus is limited. In order to investigate the genetic diversity and the distribution of C. retusus in China, 47 samples from 8 different provinces have been sequenced via restriction site-associated DNA sequencing (RAD-seq). Totally, 31, 402 high-quality single nucleotide polymorphisms (SNP) were obtained. According to the phylogenetic tree and the principal component analysis, the samples were divided into four populations, including 3 major populations and 1 hybrid population. Population1 were the samples from Jiangsu and Yunnan province and the Population2 were mainly from northern and northeast of China including Liaoning and Hubei province, while the Population4 were from Shandong and Henan province, which were in central China. As the admixture showed, the population3 were the offspring of the other 3 populations by hybridization. The mean heterozygosity of Chinese Fringe tree from different province is 0.42 %, with the highest heterozygosity, which is as high as 0.63 %, from Jiangsu province and the lowest heterozygosity, which is only 0.19, from Henan province. This is the first report about the genetic diversity and relationship of Chionanthus retusus, which will provide value information for further genetic study, genomic study, conservation and breeding.
