Daniel Neafsey, Nora Besansky and colleagues report the whole-genome sequencing of 16 anopheline mosquito species, representing a diversity of geographical locations, ecological conditions and vectorial capacities for the transmission of malaria (Science doi:10.1126/science.1258522; 27 November 2014). They also analyzed the transcriptomes from pooled male and female larvae, pupae and adults. For each species, they identify between 10,738 and 16,149 protein-coding genes. They find extensive shuffling of gene order, more frequent rearrangements on the X chromosome and high rates of gene gain or loss. In an accompanying report, Michael Fontaine, Nora Besansky and colleagues use the new genomic data to resolve the phylogeny of the Anopheles gambiae complex (Science doi:10.1126/science.1258524; 27 November 2014). They find that the ancestor of two primary malaria vectors, An. gambiae and Anopheles coluzzii, separated from other species about 2 million years ago and is distantly related to another primary malaria vector, Anopheles arabiensis. They identify pervasive autosomal introgression between these vectors, with the majority of genetic transfer in the direction from An. arabiensis into the ancestor of An. gambiae and An. coluzzii.