Genetic variations in CYP2J2 are known to contribute to inter-individual and inter-ethnic variability in response to clinical drugs, but there is no information about the genetic polymorphisms of CYP2J2 in the Wa population. We used DNA sequencing to investigate the whole CYP2J2 gene in 100 unrelated healthy Wa individuals. SIFT and PolyPhen-2 were used to predict the protein function of the novel non-synonymous mutation in CYP2J2 coding regions. Fst anlyasis and Chi-square test were used to compare genotyping data of CYP2J2 in our study Wa population with other populations around the world. We identified 14 different CYP2J2 polymorphisms in the Wa Chinese population, including three novel variant (15016G>A, 19109C>T and 33885A>T). Variant 15016G>A was predicted to be possibly damaging on protein function by SIFT and PolyPhen-2. Using the Chi-square test, we found rs11572245 in the different frequency distributions when the Wa population was compared to other eleven populations. The frequencies of rs1155002 in the Wa people are higher than most of Asia populations, but lower than most of Europe populations. Our results provide basic information about CYP2J2 alleles in Wa, which may help to optimize pharmacotherapy effectiveness by providing personalized medicine to this ethnic group.