In this systemic population‐based study on G6PD deficiency in China, we present the frequencies of G6PD deficiency and the distribution of G6PD gene variants in 12 ethnic populations, illustrating the epidemiological features, evolutionary origin and malaria‐induced positive selection effects of G6PD‐deficient alleles in China. The gene discussed is G6PD; the disease is G6PD deficiency.