Mosquito-borne diseases continue to be a burden to global health. The viruses that cause these diseases are maintained in nature through a biological transmission cycle involving susceptible vertebrate and mosquito hosts. While knowledge of the interactions occurring between mosquito-borne viruses and vertebrates is considerable, much less is known about the interactions of these viruses with their disease vectors. Studies with Drosophila melanogaster have been important in understanding how insects respond to viral infections. However, mosquitoes and the viruses they vector have co-evolved during a long period of time. Unfortunately, many of the genetic advantages of a fly model are not available when working with mosquitoes. Nevertheless, a sequenced genome, and molecular tools such as high-throughput sequencing and RNAi knockdown are helping to bridge these gaps. Here we describe several additional tools for the study of virus-vector interactions in the mosquito.