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Background  Genetic diversity studies provide evidence of  Plasmodium falciparum  differentiation that could affect fitness and adaptation to drugs and target antigens for vaccine development. This study describes the genetic structure of  P. falciparum  populations in urban and rural sites from southwestern Nigeria.    Methodology  Ten neutral microsatellite loci were genotyped in 196  P. falciparum  infections from three localities: Aramoko-Ekiti, a rural community; Lekki, an urban location and Badagry, a peri-urban border settlement. Analysis was performed on the genetic diversity, linkage disequilibrium, population structure and inter-population differentiation.    Results  Allelic diversity values were similar across all populations, with mean expected heterozygosity (H E ) values between 0.65 and 0.79. No matching multilocus haplotypes were found and analysis of multilocus LD showed no significant index of association. Genetic differentiation between populations was low (ΦPT = 0.017).    Conclusion  The absence of detectable population structure of  P. falciparum  in southwestern Nigeria is evident in the lack of significant differentiation between populations separated by about 200 km. This implies that a fairly uniform malaria control strategy may be effective over a wide geographic range in this highly endemic region. However, more wide-scale survey across the country will be required to inform malaria control in this large and densely populated endemic region.

Microsatellite markers reveal low levels of population sub-structuring of Plasmodium falciparum in southwestern Nigeria