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Highly polymorphic microsatellite markers in <jats:italic>P. falciparum<\/jats:italic> were used to investigate genetic diversity, polyclonality and genetic structure among populations in areas of varying malaria transmission intensity across Kenya. We also assessed relationships between metrics derived from genetic data, transmission intensity estimates and bioclimatic variables. Despite an overall reduction in transmission intensity across Kenya from 2005 to 2014, we found that parasite populations maintained high genetic diversity and that genetic diversity correlated more closely with past transmission intensity estimates in the year 2000 as compared to contemporary estimates in 2014. In contrast, we found genetic structuring to be significant, consistent with our observation of shifting parasite migration patterns in western Kenya. Both genetic diversity and polyclonality increased with higher precipitation in the dry season, revealing the potential impacts of changing climate patterns on parasite population dynamics. 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