Mosquitoes are primary medical insect pests due to their diseases transmission as vectors. In Korea, the insecticide-resistant populations of disease vector mosquito species, such as Anopheles sinensis, Culex pipiens and Culex tritaeniorhynchus, have constantly increased. Thus, management of insecticide resistance to major insecticides including pyrethroids and organophosphates is required for more efficient control of resistant populations. In this study, the quantitative sequencing (QS) protocols were established to detect the frequencies of three mutations (the L1014F on voltage sensitive sodium channel and the G119S and F331W on acetylcholinesterase 1) that are associated with either pyrethroids or organophosphates. Based on the QS protocol using newly designed non-polymorphic primers, resistance allele frequencies (RAFs) were estimated in field populations of An. sinensis, Cx. pipiens and Cx tritaeniorhynchus collected from an identical site in Korea. The dynamics of each resistance allele frequency over time in the same populations were also evaluated.