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Background  Despite the medical importance of mosquitoes of the genus  Anopheles  in the transmission of malaria and other human diseases, its phylogenetic relationships are not settled, and the characteristics of mitochondrial genome (mitogenome) are not thoroughly understood.    Methods  The present study sequenced and analyzed the complete mitogenomes of  An. peditaeniatus  and  An. nitidus , investigated genome characteristics, and inferred the phylogenetic relationships of 76  Anopheles  spp.    Results  The complete mitogenomes of  An. peditaeniatus  and  An. nitidus  are 15,416 and 15,418 bp long, respectively, and both include 13 PCGs, 22 tRNAs, two tRNAs and one control region (CR). Mitogenomes of  Anopheles  spp. are similar to those of other insects in general characteristics; however, the  trnR  and  trnA  have been reversed to “ trnR - trnA ,” as has been reported in other mosquito genera. Genome variations mainly occur in CR length (493–886 bp) with six repeat unit types identified for the first time that demonstrate an evolutionary signal. The subgenera  Lophopodomyia ,  Stethomyia ,  Kerteszia ,  Nyssorhynchus ,  Anopheles  and  Cellia  are inferred to be monophyletic, and the phylogenetic analyses support a new phylogenetic relationship among the six subgenera investigated, in that subgenus  Lophopodomyia  is the sister to all other five subgenera, and the remaining five subgenera are divided into two clades, one of which is a sister-taxon subgenera  Stethomyia  +  Kerteszia , and the other consists of subgenus  Nyssorhynchus  as the sister to a sister-group subgenera  Anopheles  +  Cellia . Four series (Neomyzomyia, Pyretophorus, Neocellia and Myzomyia) of the subgenus  Cellia , and two series (Arribalzagia and Myzorhynchus) of the subgenus  Anopheles  were found to be monophyletic, whereas three sections (Myzorhynchella, Argyritarsis and Albimanus) and their subdivisions of the subgenus  Nyssorhynchus  were polyphyletic or paraphyletic.    Conclusions  The study comprehensively uncovered the characteristics of mitogenome and the phylogenetics based on mitogenomes in the genus  Anopheles , and provided information for further study on the mitogenomes, phylogenetics and taxonomic revision of the genus.    Graphical abstractSupplementary Information  The online version contains supplementary material available at 10.1186/s13071-021-04963-4.

parasites and vectors

Complete mitogenomes of Anopheles peditaeniatus and Anopheles nitidus and phylogenetic relationships within the genus Anopheles inferred from mitogenomes