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Background   Aedes  mosquitoes are important invasive species contributing to the spread of chikungunya, dengue fever, yellow fever, zika virus, and other dangerous vector-borne diseases.  Aedes albopictus  is native to southeast Asia, with rapid expansion due to human activity, showing a wide distribution in the Korean peninsula.  Aedes flavopictus  is considered to be native to East Asia, with a broad distribution in the region, including the Korean peninsula. A better understanding of the genetic diversity of these species is critical for establishing strategies for disease prevention and vector control.    Methods  We obtained DNA from 148 specimens of  Ae. albopictus  and 166 specimens of  Ae. flavopictus  in Korea, and amplified two mitochondrial genes ( COI  and  ND5 ) to compare the genetic diversity and structure of the two species.    Results  We obtained a 658-bp sequence of  COI  and a 423-bp sequence of  ND5  from both mosquito species. We found low diversity and a nonsignificant population genetic structure in  Ae. albopictus , and high diversity and a nonsignificant structure in  Ae. flavopictus  for these two mitochondrial genes.  Aedes albopictus  had fewer haplotypes with respect to the number of individuals, and a slight mismatch distribution was confirmed. By contrast,  Ae. flavopictus  had a large number of haplotypes compared with the number of individuals, and a large unimodal-type mismatch distribution was confirmed. Although the genetic structure of both species was nonsignificant,  Ae. flavopictus  exhibited higher genetic diversity than  Ae. albopictus.Conclusions   Aedes albopictus  appears to be an introduced species, whereas  Ae. flavopictus  is endemic to the Korean peninsula, and the difference in genetic diversity between the two species is related to their adaptability and introduction history. Further studies on the genetic structure and diversity of these mosquitos will provide useful data for vector control.    Supplementary Information  The online version contains supplementary material available at 10.1186/s13071-021-04873-5.

Comparative population genetics of the invasive mosquito Aedes albopictus and the native mosquito Aedes flavopictus in the Korean peninsula