The wide-spread development of insecticide resistance in mosquitoes, including the deadly vector Aedes aegypti, is leading to worldwide outbreaks of mosquito-related diseases. To understand the mechanisms and genes involved in the development of insecticide resistance in Ae. aegypti, we investigated differential gene expression among multiple pyrethroid resistant and susceptible populations of Ae. aegypti using RNASeq techniques. Among the tested Aedes populations, a highly pyrethroid resistant Cas9 strain was specifically generated by genetically crossing a highly pyrethroid resistant strain to a Cas9 expressing strain, which will facilitate our functional analysis and characterization of resistance genes and mechanisms. Over 500 genes are differentially expressed between pyrethroid resistant and susceptible populations: 269 of which are upregulated while 230 are downregulated in the resistant populations. The results show a complex network of detoxification genes that are involved in pyrethroid resistance. Functional characterization of these upregulated genes in insecticide resistance in Ae. aegypti is further discussed.