The Anopheles gambiae genome project provided the community with the full sequence of this medically important disease vector. The genome sequence has already lead to the discovery of genes thought to be important for Plasmodium infection, of genes for the olfactory perception of the mosquito’s prey, and to multiple sequences of transposable elements that have proliferated in the mosquito genome. The genome has also allowed for the development of many more molecular markers that can be used in mapping, association, and population genetic studies. But the potential of the Anopheles genome cannot be fully realized without additional sequencing of other genomes: both population genomic and comparative genomic analyses will benefit from other sequenced genomes by allowing us to find those characteristics that are specific to A. gambiae and which are shared by all mosquitoes. Here I examine data from a second A. gambiae genome currently being sequenced and show how population genomic analyses can inform us about mosquito biology. I also show how data from newly sequenced dipterans, including Drosophila pseudoobscura and Aedes aegyptii, can be used to tell us about the expansion of gene families along the Anopheles lineage. Finally, I review emerging genomic technologies dependent on the A. gambiae sequence that can be used to help fight malaria.