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Background   Culex tritaeniorhynchus  and  Culex pipiens pallens  are the major vectors of the Japanese encephalitis virus and  Wuchereria bancrofti , the causative agent of filariasis. The knowledge of mitochondrial genomes has been widely useful for the studies on molecular evolution, phylogenetics and population genetics.    Methods  In this study, we sequenced and annotated the mitochondrial (mt) genomes of  Cx. tritaeniorhynchus  and  Cx. p. pallens , and performed a comparative analysis including four known mt genomes of species of the subgenus  Culex  ( Culex ). The phylogenetic relationships of  Cx. tritaeniorhynchus ,  Cx. p. pallens  and four known  Culex  mt genome sequences were reconstructed by maximum likelihood based on concatenated protein-coding gene sequences.    Results   Culex tritaeniorhynchus  and  Cx. p. pallens  mt genomes are 14,844 bp and 15,617 bp long, both consists of 13 PCGs, 22 tRNAs, 2 rRNAs and 1 CR (not sequenced for  Cx. tritaeniorhynchus ). The initiation and termination codons of PCGs are ATN and TAA, respectively, except for  COI  starting with TCG, and  COI  and  COII  terminated with T. tRNAs have the typical clover-leaf secondary structures except for  trnS   (AGN)   that is lacking the DHU stem.  16S rRNA  and  12S rRNA  secondary structures were drawn for the first time for mosquito mt genomes. The control region of  Cx. p. pallens  mt genome is 747 bp long and with four tandem repeat structures. Phylogenetic analyses demonstrated that the mt genome of  Cx. tritaeniorhynchus  was significantly separated from the remaining five mt genomes of  Culex  spp.  Culex p. pipiens ,  Cx. p. pallens  and  Cx. p. quinquefasciatus  formed a monophyletic clade with  Cx. p. quinquefasciatus  linked in the middle of the clade, and  Cx. p. pallens  should have the same taxonomic level as  Culex p. pipiens  and  Cx. p. quinquefasciatus .    Conclusions  The mt genomes of  Cx. tritaeniorhynchus  and  Cx. p. pallens  share the same gene composition and order with those of two other  Culex  species.  Culex p. pallens  of the Pipiens complex should have the same taxonomic level as  Culex p. pipiens  and  Cx. p. quinquefasciatus  investigated. We enriched the  Culex  mt genome data and provided a reference basis for further  Culex  mt genome sequencing and analyses.    Electronic supplementary material  The online version of this article (doi:10.1186/s13071-016-1694-z) contains supplementary material, which is available to authorized users.

parasites and vectors

The mitochondrial genomes of Culex tritaeniorhynchus and Culex pipiens pallens (Diptera: Culicidae) and comparison analysis with two other Culex species