Background: Vector control has been a key strategy in malaria prevention and elimination for decades. However, insecticide resistance is becoming a serious threat to vector control. Anopheles sinensis is one of the important transmission vectors for malaria in Guizhou Province, China. However, little is known on insecticide resistance status and related mechanism. In this study, the diversity and frequency of the major insecticide resistance associated genes such as voltage-gated sodium channel (vgsc) and acetylcholinesterase-1 ( ace-1 ) genes that encoded the target proteins of Pyrethroids and OPs were investigated in field populations.Methods: Adult mosquitoes were collected from 12 sampling sites across Guizhou by lamp trapping. Female An. sinensis were identified by morphological and molecular identification. Genomic DNA was extracted to amplify vgsc and ace-1 gene fragments. PCR products were sequenced bi-directly. Mutations of vgsc gene at locus 1014 and that of ace-1 at locus 119 were analyzed using MEGA 7.1 software, and the frequencies of mutations were calculated respectively.Results: 5 kdr mutation alleles at the locus 1014 of vgsc gene as a result of three amino acid replacements ( namely 1014F/C/S) in 548 samples of 12 An. sinensis populations. The total frequency of kdr mutation alleles was 27.4%, of which the TTT/C (F) allele had a highest mutation frequency of 22.5%. The top three mutation genotypes were from XiShui, TongZhi and DeJiang populations collected in north Guizhou. There were three alleles at locus 119 in ace-1 gene with 49.47% of GGC/G, 0.17% of GGT/G and 50.36% of AGC/S. The 100% frequency of mutation genotypes (GS, SS) was found in CeHeng, LuoDian and SanDu populations gathered in southwest Guizhou.Conclusion: A diverse genetic mutations of vgsc and ace-1 genes are found in An. sinensis in Guizhou. There are a significant geographical heterogeneities of allele frequency among different populations in Guizhou. A high frequency of kdr mutation (>44 %) in north Guizhou. The 119S mutation of ace-1 gene is present at a high frequency in most An. sinensis populations in Guizhou, especially in the previously highly endemic malaria regions. These findings suggest continued monitoring of the genotypic diversity of insecticides resistance genes may assist to formulate a region-customized resistance management strategies.