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Ten microsatellite loci, four located within and six outside chromosome inversions, were employed to study the genetic structure of Anopheles arabiensis across the ecological zones of Nigeria (arid savannah in the north gradually turns into humid forest in the south). Regardless of location within or outside inversions, genetic variability at all loci was characterized by a reduction in both the number of alleles per locus and heterozygosity from savannah to forest. Across all loci, all but one allele in the forest also occurred in the savannah, whereas at least 78 alleles in the savannah were missing in the forest. Genetic differentiation increased with geographical distance; consequently, genetic distances between zones exceeded those within zones. The largest genetic distances were between localities at the extremes of the transect (range F-ST = 0.196-0.258 and R-ST = 0.183-0.468) and were as large as those between A. arabiensis and Anopheles gambiae s.s. Gene flow across the country was very low, so that Nm between the extremes of the transect was <1. These data suggest that A. arabiensis has extended its range from the savannah into the forest during which it experienced a reduction in effective population size due to sequential founder effects. Gene flow post range expansion appears too restricted by geographical distance to homogenize the gene pool of A. arabiensis across Nigeria.