Overlapping measurements in the length of the genitalia of Leptidea sinapis/reali collected in Slovenia triggered an investigation of a possible natural hybridization between these two well known sibling species of butterflies. Random polymorphic DNA (RAPD) was used to generate species specific markers and sequences of the cytochrome oxidase subunit one gene for determination of the progeny. RAPD's clustering and mitochondrial DNA (mtDNA) phylogeny were congruent with the taxonomic placement of specimens of both species, but slightly incongruent with the results of the analysis of genital morphology. Two specimens with L. reali genitalia measurements, but genetically belonging to L. sinapis, had species specific RAPD markers of both species indicating probable hybrid origin. All the specimens with genitalia of intermediate length were also genetically assigned to L. sinapis indicating a possible one way introgression as predicted from their genitalia morphology. Leptidea sinapis was found predominantly in xerothermic habitats in Slovenia, whereas L. reali was more of a generalist except in the sub-Mediterranean region where it is limited to humid meadows.