Delimitation of allopatric populations into species remains subjective and largely arbitrary. Many cold-adapted species from the sub-Arctic and Central and Southern European Mountain systems provide excellent models to study allopatry problem due to their patchy distributions.The same concerns many Holarctic species, which frequently show varying degrees of differentiation between continents. In this study, we analyze high-throughput target enrichment data for 10 groups of Arctic-alpine and Holarctic lepidopteran species sampled from different regions across the Holarctic realm, i.e., Fennoscandia, European Alps, Altai Mountains, and North America. We first aimed to assess whether the genetic differences in the nuclear genome reflected observed DNA barcode divergences and, secondly, whether the gap between population and species-level differences can be reliably dissected using genomic data. We compared the phylogenetic trees and uncorrected pairwise genetic distances obtained from target enrichment and mitochondrial COI barcodes and performed a suite of population genetic and species delimitation analyses to further explore patterns of intraspecific variation in our study species. We observed that in about one-half of the cases, DNA barcodes showed phylogenetic relationships similar to the target enrichment markers. Nuclear genetic differentiation varied among the populations analyzed, from low differentiation of geographically separated populations to the deeper separation of some Nearctic populations and Arctic-alpine disjunction in the populations from Fennoscandia and Southern European mountains. Our results highlight the need for consistent delimitation of allopatric populations, especially given the prevalence of distributional discontinuities across species. Large sets of standard genetic markers provide a very promising avenue towards this goal.