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Discordance between “phylogenetic entities” revealed by mitochondrial\nuclear genes and “traditional species” recognized on the basis of morphological characters, ecological traits and distribution is a quite common phenomenon in modern taxonomic and evolutionary studies. However, the factors determining such discrepancies have received little attention despite its obvious significance for taxonomy and evolution. During the complex investigation of the Palaearctic Lepidoptera we have studied cases of incongruence between molecular markers and morphological characters for a number of taxa of the genus Colias (Lepidoptera: Pieridae) on a base of approach uniting analysis of multilocus molecular data and methods of population genetics. The most striking example of mito-nuclear discordance was found in the taxonomically well- studied species - Moorland clouded yellow (Colias palaeno). We used six gene regions (mitochondrial COI, and nuclear CAD, EF-1a, GADPH, RPS5, and wingless) to analyze the genetic structure of this species. Analysis of the COI gene revealed the presence of five highly diverged mitochondrial lineages (the genetic distance ranged from 1,5% to 9%). In contrast to this, we have found that Colias palaeno is genetically homogenous with respect to studied nuclear genes. Thus, the discovered mitochondrial lineages did not correspond neither to the phenotypic traits, nor to the clustering of nuclear genes. Simultaneously, haplotypes similar to Colias palaeno were found in other Colias species, suggesting that some of detected lineages may have appeared as a result of interspecific hybridization and mitochondrial introgression. Additionally, we found that the mitochondrial clades are strongly associated with two different Wolbachia strains, supporting the hypothesis that the mito-nuclear discordance resulted from selection on the mitochondrial genome due to selective sweeps by Wolbachia strains. We conclude that Wolbachia infection and mitochondrial introgression has played a key role in the evolution of mitochondrial genomes of Colias palaeno. The financial support for this study was provided by the grants from the Russian Foundation for Basic Research No. 18-34-00756, 17-04-00828, 17-04-00754. The work was conducted within the framework of the state task No. 6.2884.2017/4.6 Ministry of Education and Science of Russian Federation.