The M and S molecular forms of Anopheles gambiae are undergoing speciation as they adapt to heterogeneities in the environment, spreading malaria in the process. We hypothesized that their divergence despite gene flow is facilitated by reduced recombination at the centromeric (proximal) end of the X chromosome. We sequenced introns from 22 X chromosome genes in M and S from two locations of West Africa where the forms are sympatric. Generally, in both forms nucleotide diversity was high distally, lower proximally, and very low nearest the centromere. Conversely, differentiation between the forms was virtually zero distally and very high proximally. Pairwise comparisons to a close relative, the sibling species Anopheles arabiensis, demonstrated uniformly high divergence regardless of position along the X chromosome, suggesting that this pattern is not purely mechanical. Instead, the pattern observed for M and S suggests the action of divergent natural selection countering gene flow only at the proximal end of the X chromosome, where recombination is reduced. Comparison of sites with fixed differences between M and S to the corresponding sites in A. arabiensis revealed that derived substitutions had been fixed in both forms, further supporting the hypothesis that both have been under selection. These derived substitutions are fixed in the two West African samples and in samples of S from western and coastal Kenya, suggesting that selection occurred before the forms expanded to their current ranges. Our findings are consistent with a role for suppressed genetic recombination in speciation of A. gambiae.R educed recombination contributes to the persistence of species or emerging species in the face of gene flow (1, 2). Despite some interbreeding and hybrid formation, species-specific regions of the genome can be preserved from introgression and homogenization of different genetic backgrounds if they are not subject to crossing over. Recent elaborations of this concept in organisms as diverse as humans, sunflowers, fruit flies, and mosquitoes invoke chromosomal inversions because recombination is effectively suppressed between the break points of chromosomal inversion heterozygotes (3-6). If captured by inversions, genes involved in assortative mating and species-specific ecological adaptations would remain associated longer relative to the case of free recombination. For pairs of species that have diverged in parapatry or sympatry, these models predict (i) that they are likely to differ by fixed inversions, (ii) that genes involved in reproductive isolation and species-specific adaptations should preferentially map to these inversions, and (iii) that significantly greater genetic divergence will accumulate in rearranged versus colinear regions. These predictions seem to be upheld for the group of mosquito sibling species known as the Anopheles gambiae complex (7, 8) but not for A. gambiae itself.A. gambiae, the primary vector of malaria in subSaharan Africa, is undergoing speciation. The incipient species (designate...