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Background   Plasmodium falciparum  erythrocyte binding antigen-175 ( Pf EBA-175) is a candidate antigen for a blood-stage malaria vaccine, while various polymorphisms and dimorphism have prevented to development of effective vaccines based on this gene. This study aimed to investigate the dimorphism of  Pf EBA-175 on both the Bioko Island and continent of Equatorial Guinea, as well as the genetic polymorphism and natural selection of global  Pf EBA-175.    Methods  The allelic dimorphism of  Pf EBA-175 region II of 297 bloods samples from Equatorial Guinea in 2018 and 2019 were investigated by nested polymerase chain reaction and sequencing. Polymorphic characteristics and the effect of natural selection were analyzed using MEGA 7.0, DnaSP 6.0 and PopART programs. Protein function prediction of new amino acid mutation sites was performed using PolyPhen-2 and Foldx program.    Results  Both Bioko Island and Bata district populations, the frequency of the F-fragment was higher than that of the C-fragment of  Pf EBA-175 gene. The  Pf EBA-175 of Bioko Island and Bata district isolates showed a high degree of genetic variability and heterogeneity, with π values of 0.00407 & 0.00411 and Hd values of 0.958 & 0.976 for nucleotide diversity, respectively. The values of Tajima's D of  Pf EBA-175 on Bata district and Bioko Island were 0.56395 and − 0.27018, respectively. Globally,  Pf EBA-175 isolates from Asia were more diverse than those from Africa and South America, and genetic differentiation quantified by the fixation index between Asian and South American countries populations was significant (FST > 0.15,  P  < 0.05). A total of 310 global isolates clustered in 92 haplotypes, and only one cluster contained isolates from three continents. The mutations A34T, K109E, D278Y, K301N, L305V and D329N were predicted as probably damaging.    Conclusions  This study demonstrated that the dimorphism of F-fragment  Pf EBA-175 was remarkably predominant in the study area. The distribution patterns and genetic diversity of  Pf EBA-175 in Equatorial Guinea isolates were similar another region isolates. And the levels of recombination events suggested that natural selection and intragenic recombination might be the main drivers of genetic diversity in global  Pf EBA-175. These results have important reference value for the development of blood-stage malaria vaccine based on this antigen.    Supplementary Information  The online version contains supplementary material available at 10.1186/s12936-021-03904-x.

Population genetic analysis of the Plasmodium falciparum erythrocyte binding antigen-175 (EBA-175) gene in Equatorial Guinea