Background: The frequencies of Cytochrome P450 2C9 (CYP2C9) genotypes were various between populations. The aim of this study was to investigate the frequencies of the major variants of the CYP2C9 in Chinese Li minority populations. Methods: The promoter, exons and surrounding introns, and 3'-untranslated region of the CYP2C9 gene was detected by DNA sequencing to investigate in 100 unrelated healthy Chinese Li subjects. The protein function prediction was used the online tools: Sorting Intolerant From Tolerant (SIFT) and Phenotyping Version 2 (PolyPhen-2). The comparison of CYP2C9 allele frequencies in different populations were analyzed by Chi-square (chi(2)) test. Linkage disequilibrium (LD) analysis was performed using Haploview software. Results: We identified 17 different CYP2C9 single nucleotide polymorphisms (SNPs) in the Li population, including two missense mutations (3549 G > A and 42614 A > C) and two silent mutations (3514 T > Cand 50298A > T). The protein function prediction revealed the two missense mutations result in protein damaging. In addition, we detected the allele frequencies of CYP2C9 star 1, CYP2C9 star 3 and CYP2C9 star 42 were 98%, 1%, and 1%, respectively. Finally, we compared three major allelic frequency (CYP2C9 star 1, CYP2C9 star 2, and CYP2C9 star 3) between Li and other populations. We found that our results were similar to East Asians and Africans.