Mosquito control strategies have been primarily dependent on the use of synthetic chemical insecticides but its long-term stability and its tendency to bioaccumulate have fostered many environmental and human health concerns resulting in increase of resistance to chemical insecticides and rebounding vectorial capacity by mosquitoes. Botanical insecticides serve as suitable alternatives to synthetic ones as they are relatively effective, and are safe to environment, human, and animal life. In the present study, Citrus sinensis and Murraya koenigii leaf powders were tested separately on the third instar larvae of Aedes aegypti and Culex quinquefasciatus at concentrations of 0.2, 0.4, 0.6, 0.8 and 1.0%. Larval mortality was assessed after 24, 48, 72 and 96 hours and their respective LC50 values for C. sinensis were 0.69, 0.54, 0.48 and 0.36% for A. aegypti; and 0.61, 0.53, 0.44 and 0.34% for C. quinquefasciatus. For, M. koenigii, it was 1.05, 0.73, 0.38 and 0.24%; and 0.54, 0.50, 0.32 and 0.22% for C. sinensis respectively. Amongst tested two botanicals, C. sinensis was found to be more active against C. quinquefasciatus in dose and time dependent manner and the impact of phytochemicals on expression of C. quinquefasciatus protein analysed by SDS-PAGE revealed that the phytochemicals from C. sinensis suppressed the expression of certain proteins present in C. quinquefasciatus. Hence, this study confirms and recommends that use of C. sinensis and M. koenigii safe and eco-friendly and could use as an alternative to synthetic pesticides in vector control.