Malaria in South America remains a serious public health problem. Anopheles (Nyssorhynchus) darlingi is the most important malaria vector across tropical Latin America. Vector-targeted disease control efforts require a thorough understanding of mosquito demographic and evolutionary patterns. We present and analyze whole genomes of 1094 An. darlingi (median depth 18x) from six South American countries. We observe deep geographic population structure, high genetic diversity including 13 putative segregating inversions, and no evidence for sympatric cryptic taxa despite high interpopulation divergence. Strong signals of selection are plausibly driven by insecticides, especially on cytochrome P450 genes. Our results will facilitate effective mosquito surveillance and control while highlighting ongoing challenges that a diverse vector poses for malaria elimination in the Western hemisphere.