Background To propose effective public health strategies for using antimalarial drugs and prevention and control of genetic disorders, reliable epidemiological information on local population is needed.This study aimed to assess the prevalence and health impact of glucose-6-phosphate dehydrogenase (G6PD) deficiency and hemoglobinopathies in the population on malaria-endemic Bioko Island, Equatorial Guinea.Methods Blood samples from 4,144 unrelated subjects were screened for G6PD deficieny by fluorescence spot test, high-resolution melting assay and PCR-DNA sequencing from April 2012 to May 2014.In addition, 1,186 samples were randomly selected from the 4,144 subjects for detection of hemoglobin S (HbS;c.20 A>T), HbC (c.19 G>A), and α-thalassemia (α-thal) deletion by complete blood count, PCR-DNA sequencing and reverse dot blot genechip assay.Results The prevalence of malaria and anemia was 12.6% (522/4,144) and 32.8% (389/1,186), respectively.Overall, 8.7% people (359/4,144) were G6PD-deficient, 9.0% (249/2,758) males and 7.9% (110/1,386) females.The A-variants (c.202 G>A + c.376 A>G) were detected in 99.2% of G6PD-deficient individuals (356/359).Among the 1,186 subjects screened for hemoglobinopathies, 201 were HbS heterozygotes, 35 HbC heterozygotes, and 2 HbCS double heterozygotes;452 showed heterozygous-α3.7 kb deletion and 85 homozygous -α3.7 kb deletion.The overall allele frequencies for these disorders were HbS, 17.1% (n=203);HbC, 3.1% (n=37);and α-thal, 45.3% (n=622).Conclusions High G6PD deficiency in this population indicated that diagnosis and management of G6PD deficiency is crucial for current malaria control and elimination.People should be tested for G6PD deficiency before antimalarial treatment.Obligatory newborn screening, prenatal screening and counseling for these genetic disorders, especially HbS, are needed in the region.