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Background  The  Anopheles hyrcanus  group, which includes 25 species, is widely distributed in the Oriental and Palaearctic regions. Given the difficulty in identifying cryptic or sibling species based on their morphological characteristics, molecular identification is regarded as an important complementary approach to traditional morphological taxonomy. The aim of this study was to reconstruct the phylogeny of the Hyrcanus group using DNA barcoding markers in order to determine the phylogenetic correlations of closely related taxa and to compare these markers in terms of identification efficiency and genetic divergence among species.    Methods  Based on data extracted from the GenBank database and data from the present study, we used 399 rDNA–ITS2 sequences of 19 species and 392 mtDNA–COII sequences of 14 species to reconstruct the molecular phylogeny of the Hyrcanus group across its worldwide range. We also compared the performance of rDNA–ITS2 against that of mtDNA–COII to assess the genetic divergence of closely related species within the Hyrcanus group.    Results  Average interspecific divergence for the rDNA–ITS2 sequence (0.376) was 125-fold higher than the average intraspecies divergence (0.003), and average interspecific divergence for the mtDNA–COII sequence (0.055) was eightfold higher than the average intraspecies divergence (0.007). The barcoding gap ranged from 0.015 to 0.073 for rDNA–ITS2, and from 0.017 to 0.025 for mtDNA–COII. Two sets of closely related species, namely,  Anophels lesteri  and  An. paraliae , and  An. sinensis ,  An. belenrae  and  An. kleini , were resolved by rDNA–ITS2. In contrast, the relationship of  An. sinensis / An. belenrae / An. kleini  was poorly defined in the COII tree. The neutrality test and mismatch distribution revealed that  An. peditaeniatus ,  An. hyrcanus ,  An. sinensis  and  An. lesteri  were likely to undergo hitchhiking or population expansion in accordance with both markers. In addition, the population of an important  vivax  malaria vector,  An. sinensis , has experienced an expansion after a bottleneck in northern and southern Laos.    Conclusions  The topology of the Hyrcanus group rDNA–ITS2 and mtDNA–COII trees conformed to the morphology-based taxonomy for species classification rather than for that for subgroup division. rDNA–ITS2 is considered to be a more reliable diagnostic tool than mtDNA–COII in terms of investigating the phylogenetic correlation between closely related mosquito species in the Hyrcanus group. Moreover, the population expansion of an important  vivax  malaria vector,  An. sinensis , has underlined a potential risk of malaria transmission in northern and southern Laos. This study contributes to the molecular identification of the  Anopheles hyrcanus  group in vector surveillance.    Graphical abstractSupplementary Information  The online version contains supplementary material available at 10.1186/s13071-021-04971-4.

Molecular phylogeny of the Anopheles hyrcanus group (Diptera: Culicidae) based on rDNA–ITS2 and mtDNA–COII