Objective：To study and compare the genetic polymorphism difference of Lewis related fucosyltransferase-2（FUT2）and fucosyltransferase-3（FUT3）between LiSu minority and Han population in Yunnan. Methods：A total of 149 random samples were collected from LiSu minority in Yunnan. Samples were analyzed using blood typing serological method for Lewis phenotyping. All samples also undergone direct sequencing method for FUT2 and FUT3，and Chi square test was used for statistical analysis. Results：The frequency of Lewis phenotype in the 149 samples were as followed，Le（a-b+）46.3%，Le（a+b-）34.9%，Le（a-b-）18.7%. One FUT2 sequence sample demonstrated a rare allele G428A mutation that was common in Caucasian，however it was accompanied with A171G，C357T，A385T，and G739A mutation. Seven alleles mutation ponits were found in FUT3 sequencing，and C762A mutation was a new discovery. Besides functional Le allele，halotyping indicated 1 possible functional Le allele Le732（732C>T）and 8 non-functional Le alleles. Statistical analysis showed a significant difference in Se357，se357，385，se385，se357，571，se171，428，739，960，le59，le1067，le508，le59，508，between LiSu minority and Han population（P < 0.05）. Conclusion：Alleles FUT2 and FUT3 of LiSu minority in Yunnan province had a wider range of genetic polymorphism.