Resistance to pyrethroid insecticides is widespread in Indonesian Aedes aegypti (Linnaeus), the primary vector of dengue viruses. This study aims to investigate the mutations in the voltage-gated sodium channel (Vgsc) conferring pyrethroid resistance against Ae. aegypti populations from Indonesia. Molecular genotyping of mutations using polymerase chain reaction assay and direct DNA sequencing were performed at positions 989 and 1,016 in IIS6 region, and 1,534 in IIIS6 region of the voltage-gated sodium channel (Vgsc) in nine populations of Indonesian Ae. aegypti. The V1016G and S989P genotyping identified the RR genotype to be predominant in six out of nine populations of Ae. aegypti, whereas the SS genotype occurred only in minority. Interestingly, co-occurrence of the V1016G and S989P mutations was detected in the aforementioned six populations with high frequency. Genotyping of F1534C showed all nine populations exhibited the SS genotype, with merely two individuals from a population were heterozygous (RS). Significant correlations were demonstrated between the allele frequencies of the V1016G mutation and the survivability rates as well as resistance ratios in pyrethroid adult bioassays. This signifies the V1016G can contribute more to the insensitivity of Vgsc than the F1534C. Homozygous 1016G mosquitoes were likelier to survive pyrethroid exposure. Identification of underlying mechanisms resulting in insecticide resistance is advantageous in developing effective mosquito control programs in Indonesia.