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Background   Anopheles sinensis  is a major vector of malaria in China and its control is under great threat as the development of insecticide resistance. Voltage-gated sodium channel ( VGSC ) is the target of several classes of insecticides. Genetic mutations of  VGSC  have been documented to confer knockdown resistance ( kdr ) to dichlorodiphenyltrichloroethane (DDT) and pyrethroids in mosquitoes. To control this vector efficiently, it is important to know the resistance-associated genetic mutations, their distribution frequencies and genealogical relations.    Methods  Three hundreds and thirteen (313) adults of  An. sinensis  collected from nine locations across Guangxi Zhuang Autonomous Region were used. The partial sequence of the  An. sinensis  voltage gated sodium channel gene ( AS - VGSC ) containing codon 1014 was sequenced. PHASE2.1 was used to construct the haplotypes of each individual, and the accuracy of haplotypes was further confirmed by clone sequencing. The genealogical relations of  kdr  mutations in  AS - VGSC  was analysed using TCS 2.1 and Network 5.0.    Results  Sixteen  AS - VGSC  haplotypes including seven haplotypes carrying non-synonymous mutations at codon 1014, and fifty-five  AS - VGSC  genotypes were identified from 313 mosquitoes collected from nine geographical locations across Guangxi. The number of haplotypes in each of the nine populations ranged from 5 to 13. The frequency of haplotypes carrying  kdr  mutations ranged from 2.7 to 80.0 % within the nine populations, of which 1014C was unexpectedly high in the northeast of Guangxi. Genealogical analysis suggested multiple origins of  kdr  mutations in  An. sinensis .    Conclusion  Diverse haplotypes of  AS - VGSC  are distributed in Guangxi. The presence of haplotypes carrying mutations at codon 1014 indicates a risk of pyrethroid and DDT resistance. The  kdr  mutations show differential distribution geographically, with high frequencies occurred in the northeast of Guangxi. Genealogical analysis suggests multiple origins of  kdr  mutations in  An. sinensis  populations in Guangxi. These findings have important practical implications for the sustainability of  An. sinensis  control programmes.    Electronic supplementary material  The online version of this article (doi:10.1186/s12936-016-1467-3) contains supplementary material, which is available to authorized users.

Diversity and frequency of kdr mutations within Anopheles sinensis populations from Guangxi, China