The focus of this study was to understand the evolutionary relationships and taxonomy of widely distributed parapatric pair of Saturnia pavonia and Saturnia pavoniella (Lepidoptera: Saturniidae) in Europe. To address species delimitation challenges associated with many parapatric taxa, target enrichment and mtDNA sequencing was employed alongside analyses of admixture, gene flow, hybridization, and introgression. The dataset included individuals from both species as well as two hybrids from and broadly outside the contact zone. Nuclear markers strongly supported both S. pavonia and S. pavoniella as two distinct species, with the hybrids grouping together as intermediate and separate from both species. However, the maximum likelihood (ML) tree generated from mtDNA sequencing data presented a different picture, showing both taxa to be phylogenetically intermixed. This inconsistency may be attributed to mitonuclear discordance, which can arise from biological factors (e.g., introgressive hybridization or incomplete lineage sorting) or operational factors (e.g., misidentification or incorrect species delimitation). We further discuss our results from evolutionary point of view taking into consideration the past climatic oscillations that has likely shaped the present dynamics between the species. Overall, this study demonstrated the effectiveness of the target enrichment approach in resolving the phylogenetic relationships and providing insights into the taxonomic and phylogenetic relationships between these species.