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Anopheles gambiae  and  An. arabiensis  are major malaria vectors in sub-Saharan Africa. Knowledge of how geographical factors drive the dispersal and gene flow of malaria vectors can help in combatting insecticide resistance spread and planning new vector control interventions. Here, we used a landscape genetics approach to investigate population relatedness and genetic connectivity of  An. gambiae  and  An. arabiensis  across Kenya and determined the changes in mosquito population genetic diversity after 20 years of intensive malaria control efforts. We found a significant reduction in genetic diversity in  An. gambiae , but not in  An. arabiensis  as compared to prior to the 20-year period in western Kenya. Significant population structure among populations was found for both species. The most important ecological driver for dispersal and gene flow of  An. gambiae  and  An. arabiensis  was tree cover and cropland, respectively. These findings highlight that human induced environmental modifications may enhance genetic connectivity of malaria vectors.

Ecological drivers of genetic connectivity for African malaria vectors Anopheles gambiae and An. arabiensis