The voltage gated sodium channel is the primary target site of pyrethroid insecticides and its insensitivity has been associated with pyrethroid resistance in agriculturally and medically important insects, including mosquitoes. A mutation of leucine to phenylalanine resulting from a single nucleotide polymorphism (SNP), TTA to TTT, termed the kdr mutation, in the sodium channel gene has been associated with the insensitivity of the gene to pyrethroids. We conducted a systematical study of variation of the kdr allele expression within and among susceptible and resistant populations of Cx. quinquefasciatus by comparison of genomic DNA and RNA expression levels of corresponding individuals. We showed here a strong correlation of transcriptional regulation of allelic expression in the kdr locus through RNA allelic variation and RNA editing with the levels of pyrethroid resistance. This study indicates approaches for connecting genotype-resistance phenotype relationship based on the change in the gene expression and is the first to reveal the kdr allelic variation in sodium channel gene expression as a molecular mechanism involved in the evolution of kdr-mediated pyrethroid resistance in mosquitoes.