Background In absence of effective and safe vaccines or drugs against mosquito-borne arboviral diseases (such as dengue, Zika and Rift Valley and West Nile), there have been an increasing pattern of insecticide use against the mosquito vectors of these diseases in integrated vector management (IVM) programs in Saudi Arabia. However, the efficacy of IVM programmes is threatened by the development of insecticide resistance in vectors. 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 in Saudi Arabia. Culex quinquefasciatus is a second example as one of the major arboviral vectors in the region and a proven vector of Rift Valley fever and wide-spread in Jeddah and the rest of the western region of Saudi Arabia. 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 and Cx. quinquefasciatus 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.Results Our findings showed that Ae. aegypti resistance-associated VGSC gene mutations revealed polymorphic mutations on the 989 (allele frequency = 65.91%), 1016 (allele frequency = 65.91%), and 1534 (allele frequency = 52.27%) 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.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, and the first report of insecticide resistance gene mutation being present in field caught Cx. quinquefasciatus in Jeddah, Saudi Arabia. High prevalence of insecticide resistance gene mutations in local primary mosquito vector species, implies that the local Ae. aegypti mosquitoes are resistant to both pyrethroid and DDT, while the resistance to all four insecticide groups may possessed in Cx. quinquefasciatus populations. Our findings alert the urgent need to carry out a comprehensive insecticide resistance gene mutation surveillance and monitoring to guide sustained and effective IVM planning and innovative guidelines in local predominate mosquito populations and mosquito-borne disease control and elimination in Saudi Arabia.