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Malaria is an endemic disease in a large part of Colombia, and the city of Buenaventura reports one of the highest malaria infection rates. Some genetic variants confer resistance to malaria, such as the heterozygote for hemoglobin S (HbS) and the homozygous variant FYBES/FYBES of the Duffy gene. The aim of this work was the molecular characterization of these genes in an afrodescendent population from the urban area of Buenaventura. A total of 819 individuals from a stratified random sampling in each of the 12 communities of this city were analysed. Molecular analysis was performed using PCR-RFLP, and data analysis was performed using the Arlequin 3.5, SPSS 20 and R 3.4.1 programs. Frequencies of 3.1% and 72.2% were obtained for the S and FYBES alleles, respectively, and the values were 6.1% and 55% to AS and FYBES/FYBES genotypes respectively. The highest proportion of these resistance genotype (genotypic combination AA*FYBES/FYBES) were showed for the group of 13 to 27 years with (8.2%) and the communities 1 and 3 (18% and 10.3%, respectively). Therefore, it would be pertinent to consider these communities and age groups when performing epidemiological studies and preventive and health care campaigns on malaria in the urban areas of the city of Buenaventura.