BackgroundThe assessment of the genetic diversity of Plasmodium falciparum parasites from various malaria transmission settings could help to define tailored and dedicated local strategies for malaria control and elimination. To date, this information is scarce in Madagascar. To fill this gap, a study aiming at investigating the genetic diversity of P. falciparum populations in three epidemiological facies (Equatorial, Tropical and Fringes) in Madagascar was conducted.MethodsTwo hundred sixty-six P. falciparum isolates were obtained from patients with uncomplicated malaria enrolled in clinical drug efficacy studies conducted in health centers at Tsaratanana (Equatorial facies), Antanimbary (Tropical facies) and Anjoma Ramartina (Fringes) in 2013 and 2016. Parasite DNA was extracted from blood samples collected prior antimalarial treatment. Plasmodium species were identified by nested-PCR targeting 18S rRNA gene. The genetic profiles of P. falciparum parasites were defined by assessing the polymorphic regions of the msp-1 and msp-2 genes using allele-specific nested-PCR.ResultsA total of 58 alleles were detected for msp-1 (18 alleles) and msp-2 (40 alleles) among P. falciparum samples tested. K1 (62.9%, 139/221) and FC27 (69.5%, 114/164) were the most predominant msp-1 and msp-2 allelic families, although the proportions of the msp-1 and msp-2 alleles varied significantly between sites. Polyclonal infections were more frequent in site located in the Equatorial facies (69.8%) compared to sites in the Tropical facies (60.5%) and Fringes (58.1%). Population genetic measures showed that the genetic diversity was similar between sites and the parasite flow within sites was limited.ConclusionThis study provides recent information on the genetic diversity of P. falciparum populations in three transmission facies in Madagascar and valuable baseline data to further evaluate the impact of the control measures implemented in Madagascar.