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Background  Dengue is a serious arboviral disease in Sri Lanka with a large number of dengue fever (DF) cases every year. Control of the primary vector  Aedes aegypti  depends upon larval habitat source reduction and insecticide application. However, increases in the number of reported cases suggest the inefficiency of current control strategies and the possibility of resistance to currently used insecticides. Early detection of mutations in the voltage-gated sodium channel ( vgsc ) gene that confer knockdown resistance ( kdr ) to pyrethroid insecticides is important in resistance management in vector populations.    Results  Resistance to pyrethroid insecticides was detected in the three populations studied. Polymerase chain reaction was used to detect the presence of two  kdr  mutations F1534C and V1016G. During this process a S989P mutation was also detected in pyrethroid-resistant  Ae. aegypti  populations. These mutations were found to be widespread and frequent in the collections studied.    Conclusions  To our knowledge, this study reveals for the first time the presence of V1016G and S989P mutant alleles in the  vgsc  of Sri Lankan  Ae. aegypti  populations. The spread of the mutant alleles throughout the country poses a threat of increased resistance to pyrethroids. Long-term insecticide applications and indiscriminate use of pyrethroids has led to the evolution of resistance. More strategic and diverse strategies, including novel insecticides with new modes of action and community participation, should be engaged for  Ae. aegypti  control.    Electronic supplementary material  The online version of this article (10.1186/s13071-018-3113-0) contains supplementary material, which is available to authorized users.

First report of V1016G and S989P knockdown resistant (kdr) mutations in pyrethroid-resistant Sri Lankan Aedes aegypti mosquitoes