Background: Gene mutations on target sites can be a valuable reference to the status of insecticide resistance. Jeddah, a global commercial and major port-of-entry city, is bearing the most (>70%) dengue disease burden and the population of the dengue vector Aedes aegypti (Linnaeus, 1762) in Saudi Arabia. Culex quinquefasciatus Say, 1823 is a second example as one of the major arboviral vectors in the region. However, the status of insecticide resistance and targeted site mutations on the responsible genes are not fully characterized.Methods: We randomly sampled both mosquito species, Ae. aegypti (25 individuals) and Cx. quinquefasciatus (24 individuals) across Jeddah by daily mosquito surveillance in 2016 to detect the resistance-associated target site mutations on the voltage gated sodium channel (VGSC) and acetylcholinesterase 1 (ace-1) genes by PCR amplification and direct sequencing. Results: Our findings showed that Ae. aegypti resistance-associated VGSC gene mutations revealed polymorphic mutations on the 989, 1016, and 1534 sites. Additionally, we documented two types of introns between exons 20 and 21, however, the I1011M point mutation was undetected. Linkage disequilibrium associations were shown between V1016G with S989P, V1016G with F1534, and V1016G with type A intron. Furthermore, no mutation on ace-1 was identified in Ae. aegypti. In Cx. quinquefasciatus, homozygous L1014F/L1014F (95.23%) on the VGSC and heterozygous G119/G119S (100%) on ace-1 were widely distributed in the samples studied. Analysis of intron sequences obtained in our study and homologous sequences retrieved from GenBank showed that the intron type was significantly associated with 1016 (P = 0.000) allele type, and may reflect the history of insecticide treatment in different continents.Conclusions: To the best of our knowledge, this is the first record of the intron types between exons 20 and 21 on VGSC of Ae. aegypti populations. It can serve as a reference marker to evaluate the local insecticide resistance status. In addition, the first report of insecticide resistance gene mutation being present in field caught Cx. quinquefasciatus in Saudi Arabia. High prevalence of insecticide resistance gene mutations in local primary mosquito vector species alert the urgent need to carry out a comprehensive insecticide resistance surveillance.