Exploring the molecular genetics relationships between Han subpopulations in different administrative regions of China are always noticed by academics. Short tandem repeat (STR) has been often used in molecular genetics studies. The cluster analysis

principal component analysis and MCOA analysis had been used in this paper

we focused on the nine common STR loci (D8S1179

D21S11

D7S820

D3S1358

D13S317

vWA

D18S51

D5S818

FGA) allele frequency data of Han subpopulations from 32 administrative regions in China

in order to initially explore the molecular genetics relationships

the spatial distribution characteristics and distribution pattern of the Chinese Han subpopulations. The studies revealed that the Han nationality could be segregated into two groups which are the Southern and the Northern Han by the Yangtze River. In the Northern areas of China

the Han subpopulations from Shandong and Tianjin have large genetic distance with others; In the Southern areas

the genetic relationships within the Han subpopulations of Hong Kong

Hainan and Guangxi are much closed and greatly different from the others. The Han subpopulation of Xiamen is comparatively closed to Northern Han. Principal component scatter plot reflects that the spatial distribution pattern of Han subpopulations is wide distribution and gathered tightly in small areas in China. The three main factors contributing to the distribution characteristics of Han subpopulations in China are geographic isolation by the Yangtze River

floods in history and the population migration caused by wars or disasters using MCOA analysis method.