We assess the potential of complete coding sequences of the mitochondrial cytochrome oxidase genes (COI and COII) and the intervening tRNA-Leucine gene for use in mosquito higher-level systematics, and apply this data to an outstanding question: the phylogenetic affinities of Toxorhynchites. Traditionally placed in its own subfamily and regarded as sister group to Culicinae, recent morphological data instead have suggested that this distinctive genus belongs well within the Culicinae. Published molecular systematic studies seemingly conflict with this new morphological data or are ambiguous. The mitochondrial gene data that we present show good potential for elucidating suprageneric relationships in Culicidae, and strongly support the placement of Toxorhynchites well within the Culicinae. Reexamination of published data sets suggests that there is no substantive conflict among data sets on this issue.