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Natural hybridization is rather widespread and common in animals and can have important evolutionary consequences. In terms of taxonomy, exploring hybridization and introgression is crucial in defining species boundaries and testing taxonomic hypotheses. Butterfly specimens with unusual morphological characters (e.g., unusual wing coloration) have contradictory interpretations in the literature and have been considered by different authors either as previously undescribed taxa, putative hybrids, or aberrations of well-known species. Such individuals clearly represent a taxonomic problem that needs to be addressed by scientists. The application of molecular techniques could shed light on the origin of morphological uncertainty. Here we describe the morphology of two pierid butterflies collected in Kyrgyzstan and Iran with unusual wing pattern, which are thought to represent naturally occurring hybrids due to their intermediate phenotype. We employed one mitochondrial marker (COI gene) and three nuclear markers (Ca-ATPase, H3, and CAD genes), as standard phylogenetic markers, to test the hypothesis of the hybrid origin of these specimens and to identify the direction of the introgression. We confirm hybrid origin of the specimens in question and indicate that the specimens are wild-caught hybrids between female of Colias christophi helialaica and male of Colias cocandica, as well as between female of Colias sagartia and male of Colias aurorina. Our study shows that application of unlinked molecular marker analysis, namely mitochondrial and nuclear DNA genes, can successfully discriminate natural hybrids in the taxonomically complicated genera of butterflies, such as Colias.