Evidence for introgression between Anopheles gambiae and An. arabiensis has accumulated for some time. We examined the fate of introgressed DNA directly, using microsatellite markers located throughout the genome. Introgressed X chromosomes were removed within two generations. Furthermore, substantial differences in introgressive capacity between the two autosomes were found. After introgression from An. arabiensis into An. gambiae, most introgressed alleles at third chromosome markers, particularly those on 3R, decreased steadily, indicating selection against them. No such pattern was observed for 2L markers and several 2P markers. The frequency of introgressed alleles on 2L were close to the original frequency even after 19 generations, whereas only two 21? markers showed a modest decrease. Even though limited information was available on the reciprocal cross, the pattern appears to be identical. Although the decrease in frequency of the introgressed X chromosome can be attributed to the presence of sterility and inviability effects, the variation in introgressive capacity of the autosomes does not appear to be explained by the presence of inversion polymorphisms, or regions causing hybrid sterility and inviability. These results can have some important implications for the spread of insecticide resistance and the control of these vector populations via the release of transgenic mosquitoes.