Mosquitoes (Diptera: Culicidae) offer a unique opportunity to study evolution at multiple levels of divergence. This opportunity is facilitated by extensive research into a few species that contribute to disease transmission, and has uncovered prevalent subpopulation structure in many. Anopheles gambiae, one of the important vectors of malaria in sub-Saharan Africa, is one such species in which subdivision has been recorded, as both the molecular forms M and S and as chromosomal ecotypes. Understanding evolutionary relationships within and between species requires understanding both how divergence has proceeded in the past and what are modern forces shaping divergence in the present.  To this end, I began by generating a phylogeny of Culicidae, incorporating both morphological and molecular markers. Strongly supported relationships include the basal location of subfamily Anophelinae, along with internal organization of the tribes Aedini and Sabethini of subfamily Culicinae. Yet, despite including representatives from 25 of 44 Culicid genera, other relationship within Culicinae could not be resolved due to the ancient, rapid nature of their diversification.  Next, we proceeded to examine subpopulation divergence within An. gambiae. First, we explored patterns of genomic divergence between co-localized M and S populations from western and central Africa, hybridized to a SNP genotyping array. The pattern of M:S divergence is highly conserved across Africa. Furthermore, regions of high M:S divergence are interspersed with regions that cluster based on geographic origin, indicating gene flow is still occurring. We offer a hypothesis to explain the maintenance of such high divergence regions in the face of gene flow, namely, that occasional relaxation of environmental selective pressures allows temporary periods of introgression between sympatric M and S populations.  For my final chapter, focus was switched to the 2La inversion polymorphism in An. gambiae, which is associated with desiccation resistance. We searched for potential phenotypic differences in the cuticle thickness and cuticular hydrocarbon composition between mosquitoes differing in their 2La inversion status, raised in either normal conditions or following aridity acclimation. Few significant differences were found in cuticle thickness. We did, however, find significant differences in arid reared mosquitoes relative to normal reared, regardless of inversion status, in the relative proportion of higher chain hydrocarbons. Studies in Drosophila melanogaster indicate that such differences may be adaptive in nature in terms of heat tolerance, and suggest that further investigations into this area may prove fruitful.