BackgroundAedes albopictus is distributed widely in China, as a primary vector of Dengue fever and Chikungunya fever in south of China. Chemical insecticide control is one of the integrated programmes to prevent mosquito-borne diseases. Long-term applications of pyrethroids have resulted in the development of resistance in Ae. albopictus populations in China. However, the susceptibility of Ae. albopictus to pyrethroids in Hainan Island was unclear. Knockdown resistance (kdr), caused by point mutations in the VGSC gene, is one of the mechanisms that confer resistance to DDT and pyrethroids. This study was to investigate the resistance level of Ae. albopictus populations in Haikou City to three pyrethroid insecticides, and elucidate the relationship between the resistant phenotype and kdr mutations.MethodsThe Aedes albopictus samples were collected in Xinbu Island (XI), Longtang Town (LT), Shishan Town (ST), Baishamen Park (BP), and Flower Market (FM) from Haikou City, Hainan Island, China. The larval susceptibility to deltamethrin, permethrin and beta-cypermethrin was tested by larval bioassays, and adult susceptibility to deltamethrin and DDT was determined by adult bioassays. The degree of resistance was determined by resistance ratio value (RR50 > 3) for larvae and by mortality for adult. The kdr alleles at codon 1534 of the VGSC gene were genotyped. The relationship between kdr genotypes and resistant phenotypes was analyzed by Chi-square test.ResultsOut of five populations, assessed by larval bioassays, XI was susceptible to deltamethrin and permethrin; LT was susceptible to permethrin and beta-cypermethrin; and ST was susceptible to permithrin. FM and BP both were resistant to all of the three pyrethroids, and FM showed the highest degree of resistance, with RR50 values from 65.17 to 436.36. A total of 493 individuals from the larval bioassays were genotyped for kdr alleles. Five alleles were detected, including two wildtype alleles, TTC(F) (67.04 %) and TTT(F) (0.41 %), and three mutant alleles, TGC(C) (0.30 %), TCC(S) (31.54 %) and TTG(L) (0.71 %). There was a clear correlation between mutant alleles (or F1534S) and resistant phenotypes (P < 0.01).ConclusionTwo novel kdr mutant alleles F1534S and F1534L were detected in the pyrethroid resistant populations of Ae. albopictus in Haikou Hainan, China. For the first time, the mutant F1534S was associated with pyrethroid resistance in Ae. albopictus.Electronic supplementary materialThe online version of this article (doi:10.1186/s40249-016-0125-x) contains supplementary material, which is available to authorized users.