To determine the incidence and molecular characteristics of G6PD deficiency in Chaozhou region of eastern Guangdong Province. G6PD enzyme activity was assayed with an auto-bioanalyzer. Reverse dot blotting (RDB) was used for detecting 6 common G6PD mutations. Samples with no mutation detected by RDB were further sequenced for unknown mutations. The rate of G6PD deficiency was 3.36% (142/4224). 2.33% (47/2013) of males and 4.3% (95/2208) of females were affected. 12 mutations were detected among the 142 patients, which included c.1376G>T, c.1388G>A, c.1024C>T, c.392G>T, c.871G>A, c.95A>G, c.517T>C, c.131C>G, c.1376G>T/c.517T>C, c.871G>A/IVS-1193T>C/c.1311C>T, c.1376G>T/IVS-11, 93T>C/c.1311C>T and c.1376G>T/c.486_34delT (rs3216174). The incidence of G6PD deficiency in Chaozhou region was lower than that of the Hakka population of Guangdong Province, and the mutation types were diversely distributed in this region. c.1376G>T, c.1388G>A and c.1024C>T were the most common mutations, which was followed by c.517T>C. In addition, c.131C>G has been first discovered in the Chinese population. c.1376G>T/c.517T>C and c.1376G>T/c.486_34delT(rs3216174) were new types of compound heterozygous mutations in females.