Preliminary results from DNA-barcoding of Scandinavian butterflies and moths show high intraspecific sequence differences in the Autumnal moth, E. autumnata. One theory that might explain this finding is that E. autumnata comprises of several cryptic species. In this study, Epirrita samples from different locations in Norway, and some samples from Finland and Scotland were investigated, hoping to resolve the discrepancy found between mtDNA divergence and present division to species. The Small Autumnal moth, Epirrita filigrammaria, which is presumed to be endemic to Great Britain, was also examined because there is some suspicion of E. filigrammaria being an upland ecotype of the circumpolar E. autumnata. Sequencing of the mitochondrial region COI, as well as the nuclear regions ITS2 and Wingless, was performed. Genital preparations were made to see if morphological examinations supported the results from the molecular analysis. The results from genetic and morphological analysis showed no discrimination between E. autumnata and E. filigrammaria and support the theory of E. filigrammaria being an ecotype of E. autumnata. Results from sequencing the COI region suggest five different subgroups within the E. autumnata complex, and with no geographical structure. Sequencing of the nuclear markers and the morphological examinations shows little to no variation, and gives no indications of E. autumnata comprising of more than one species. As parasitic endosymbionts like Wolbachia is common in arthropods, all samples were sequenced with WSP primers. These results showed that several samples examined in this study were infected with Wolbachia, and with different strains corresponding to two of the mtDNA haplotypes found within E. autumnata. This might indicate indirect selection/selective sweeps on haplotypes. From these findings, a likely explanation for the high variation found within E. autumnata mtDNA is that variation arisen in allopatry, has at least partially been maintained by selective sweeps from multiple Wolbachia infections.