Gene expression during embryogenesis impacts adult mosquito fitness, the ability of an organism to survive and transmit its genotype to offspring as compared to competing organisms. Sequencing of the Ae. aegypti genome has made possible the characterization of many genes, but analysis of developmental genes has proven challenging, largely as a result of technical difficulties encountered when manipulating mosquito embryos. First, techniques that focused on handling/manipulation of embryos and various analytics were designed (Chapter 2). With these techniques I was able to properly rear, fix, stain and perform functional analyses on embryos. Even with these techniques, genes important to organismal development remained fairly uncharacterized. Second, we used comparative genomics to study genes in Ae. aegypti that are found to be homologous to developmental genes in Drosophila melanogaster, a genetic model organism. Doing so I was able to show that Netrin/Frazzled signaling at the CNS midline was conserved (Chapter 3) between the mosquito and fruit fly. I showed via RNAi, immunohistochemistry and in situ hybridization that frazzled (fra) expression is important for proper axon guidance. In D. melanogaster axon guidance genes are known to control salivary gland migration during development. Salivary glands are critical to disease transmission in mosquitoes. Although there was a level of gene conservation shown in CNS development, development of the salivary glands is different (Chapter 4). Lastly, there are populations of Ae. aegypti, that show differences in susceptibilities to pathogens. The noticeable physiological difference between the two is body size. Body size in all organisms is controlled by Insulin Signaling (IIS). Developmental stressors are shown to decrease overall body size, but increase longevity and pathogen resistance. Stress during development modulates IIS. Stress Signaling is activated by c-Jun N-Terminal Kinase (Jnk) and regulated by Puckered (Puc) phosphatase. I found the smaller less susceptible Moyo-R subpopulation expresses higher levels of jnk at all stages of development when compared to the larger more susceptible Moyo-S subpopulation (Chapter 5). In future studies, we intend to show RNAi of puc in Moyo-S will lead to smaller and less susceptible mosquitoes.