Objective　 To elucidate the molecular basis of G6PD deficiency in the Han and Li nationalities in Hainan, China. Methods　 Polymerase chain reaction and restriction enzyme digestion were used to screen the mutations 1388G→A, 1360C→T, 1024C→T, 592C→T,517T→C, 493A→G,487G→A,392G→T and 95A→G. Single strand conformation polymorphism analysis was used to screen the other mutations followed by DNA sequencing to characterize the mutations of the samples with abnormal SSCP bands. Results　 Of the fifty-nine Han cases with G6PD deficiency, fourteen with 1388G→A(23.7%), three with 871G→A(5.1%), one with 835A→T(1.7%), one with 517T→C(1.7%), three with 392G→T(5.1%), and four with 95A→G(6.8%) were found. Of the thirty-two Li cases with G6PD deficiency, six with 1388G→A(18.8%), three with 871G→A(9.4%), and two with 95A→G(6.3%) were found. A new mutation 835A→G which causes the substitution of Ala for Thr at 279 in a Han case was identified and named as G6PD-Haikou. The enzyme activity of the variant is about 10% of the normal and lower than the activity of the variant 835A→T with about 40% of the normal. Analysis of the 3D model of human G6PD has revealed that the hydroxyl group of Thr at 279 is a group in maintaining the interaction of the G6PD subunits. Conclusion　 The most common mutations of G6PD deficiency in Han and Li nationalities in Hainan are similar. Compared with the mutation spectrum of G6PD gene in the populations in other regions of China, the results indicate that some G6PD gene mutations are widespread in the populations of different regions in the southern part of China. The hydroxyl group of the Thr at 279 of human G6PD may be a necessary group for maintaining the interaction of the G6PD subunits and the enzyme activity.