Currently, dengue has became a major public health problem in Indonesia. Aedes aegypti is confirmed as the main dengue vector. The organophosphate and phyretroid have been used in vector control program for more than 3 decades. Insecticide resistance evidences and mechanisms are essential to find the current status of insecticide susceptibility of dengue vectors. In this study, we analyzed the molecular principles of resistance to phyrethroid and organophosphate insecticides on mosquitoes collected from Palu, Central Sulawesi, and Belu and Ende, East Nusa Tenggara. Single-step polymerase chain reaction (PCR) method was conducted to detect amino acid mutations in paratype voltage-gated sodium channel (VGSC) gene and Achetylcoline esterase-1 (AChE) gene of Ae. Aegypti mosquitoes. The result showed that V1016G mutations of VGSC gene were detected from the wild-caught Ae. Aegypti mosquito from Palu, Belu and Ende. In contrast, G119 wild type allele of AChE gene was found from all Ae. Aegypti of all study sites. These evidences suggest that Ae. aegypti from Palu, Belu and Ende have developed multiple resistance towards phyrethroid insecticides. Based on prior susceptibility test, Ae. aegypti from all study sites were possibly developing resistance to organophosphate in other mechanisms. New strategies are needed, especially insecticide rotation in this area to achieve efficient vector control.