Aim: To investigate the phylogeography and genetic structure of the long-fingered bat (Myotis capaccinii) across Europe using mitochondrial DNA and ddRAD-seq data, and to investigate, using high-resolution SNP data, whether the previously recorded mito-nuclear discordance in the species reflects a biological reality or was due to the low resolution of the nuclear microsatellites used in earlier studies. Location: Europe, including Northern Africa, Iberian Peninsula, Italy, Balkans, Anatolia, and the Near East. Taxon: Myotis capaccinii (long-fingered bat), a widely distributed bat species in the Mediterranean region. Methods: A total of 265 wing tissue samples were collected from 40 sites across 10 countries. Mitochondrial cytochrome-b sequences were analyzed for haplotype diversity and phylogenetic relationships. ddRAD-seq was performed on 144 samples to obtain nuclear SNPs. Phylogenetic trees, haplotype networks, Bayesian skyline plots, mismatch distributions, AMOVA, and STRUCTURE analyses were used to infer genetic structure and historical demography. Results: Three distinct mitochondrial clades (B, C1, C2) were identified, with divergence times estimated at ~350K and ~120K years BP. Clade B showed a star-like haplotype network and highest diversity, suggesting refugial origin in Anatolia. ddRAD-seq data corroborated mtDNA results and revealed longitudinal patterns of postglacial expansion and admixture. STRUCTURE analysis supported clustering into two or three genetic groups with admixture zones. Bayesian skyline plots indicated recent population expansions during the Holocene. Main conclusions: The genetic structure of Myotis capaccinii reflects historical isolation in glacial refugia followed by postglacial expansions. Integrative use of mtDNA and ddRAD-seq data effectively resolved phylogeographic patterns and mito-nuclear discordance. Mountain ranges acted as barriers to female gene flow, while nuclear data revealed ongoing interbreeding. This study highlights the importance of combining genomic approaches to understand evolutionary history and inform conservation strategies.