Background : There have been many reports on the population genetic structure of Plasmodium falciparum from different endemic regions especially sub‑Saharan Africa. However, few studies have been performed on neglected populations, such as the Pygmy populations. In this study, the population genetic structure of P. falciparum was inves‑tigated in the Baka Pygmies of Gabon and compared to that observed in neighboring villages composed mostly of Bantu farmers. Methods : A total of 342 blood samples were collected from 170 Baka Pygmies and 172 Bantus in the north of Gabon (Woleu Ntem Province). Plasmodium infections were characterized by sequencing a portion of the parasite cytochrome b gene. Population genetic structure of P. falciparum in the different villages was analysed using microsat‑ellite markers and genes coding for antigenic proteins (MSP1, MSP2, GLURP, and EBA‑175). Results : Overall, prevalence of P. falciparum was around 57% and no significant difference of prevalence was observed between Pygmies and Bantus. No significant differences of population genetic structure of P. falciparumwas found between Pygmy and Bantu people except for one antigen‑coding gene, glurp, for which genetic data suggested the existence of a potentially disruptive selection acting on this gene in the two types of populations. The genetic structure of P. falciparum followed a pattern of isolation by distance at the scale of the study. Conclusion : The prevalence and genetic diversity of P. falciparum observed in Baka demonstrates a significant transmission of the parasite in this population, and some exchanges of parasites with Bantu neighbours. Despite that, some antigen‑coding genes seem to have had a particular evolutionary trajectory in certain Pygmy populations due to specific local human and/or mosquito characteristics.