In order to study the frequency of 9 bp deletion of mtDNA V region and polymorphisim of Ychoromosome DYS287 sites among Uighur population in eight geographical regions of Xinjiang. We used the polymorphism of DYS287 sites in Y choromosome and the defeciency frequency of chromosome DNA 9 bp region by PCR directly sequensing method and by PCR combining with agarose gel electrophoresis respectively.The results showed: Among 240 unrelated modren Uighur individuals who come from Kashgar

Khotan

Kuqa

and Qarqan

Hulja

Hami

Turpan

and Lopnur in XinJiang

the frequency of 9 bp deletion of mtDNA value as 4%，3.7%，3%，4%，4.5%，4%，3%，4% Polymorphisim of Ychoromosome DYS 287 sites of 180 modern Uighur male individuals all appears as YAP-，none shows YAP＋. The results suggest that Uighur groups in different parts of Xinjiang show very low frequency in their 9 bp deletion of mtDNA

9 bp deletion is not a modern Uighur matrilineal genetic structure of transfer

Uighurs in different region of Xinjiang share same 9 bp deletion of mtDNA. Paternal genetic structure is simple

YAP + is not a modern Uighur population genetic characteristics of the male line.So

some conclusions can be given:with collecting frequency of 9 bp deletion of mtDNA and polymorphisim of Ychoromosome DYS 287 sites of Uighur population in different regions of Xinjiang

conduct analysis genetic relationship of Uighur population in different region of Xinjiang and Forensic identification provide some background informations about origin relationship Uighur groupsin different regions.