Abstract: The distribution of MYS2 polymorphism in 26 Chinese populations was analyzed by PCR. And the variations of intra- and between populations were calculated using AMOVA by Arlequin Package. MYS2＊4 was the common allele while the incidence of MYS2＊3 was much different in these pop- ulations. By AMOVA, 7. 76 %、8. 11 % and 1. 42 %of total variation were found among all 26, 10 Southern and 16 Northern Chinese populations respectively. And 4. 34 %of total variation was found between the Southern and Northern groups while 1. 57 %was found between northeast and northwest groups. The results showed that MYS2 polymorphism is very useful in analyzing the genetic structure of Chinese population. Some difference in genetic structure was seen among the different populations and a geographical distinction between South and North was confirmed. The distinction between Western and Eastern populations in the Northern China was also suggested.

Key words: Y chromosome; MYS2; AMOVA; Chinese populations