A problem to implement conservation strategies is that in many cases recognized taxa are in fact complexes of several cryptic species. Failure to properly delineate species may lead to misplaced priorities or to inadequate conservation measures. One such species complex is the yellow-spotted ringletErebia manto, which comprises several phenotypically distinct lineages, whose degree of genomic isolation has so far not been assessed. Some of these lineages are geographically restricted and thus possibly represent distinct units with conservation priorities. Using several thousand nuclear genomic markers, we evaluated to which degree thebubastislineage from the Alps and thevogesiacalineage from the Vosges, are genetically isolated from the widespreadmantolineage. Our results suggest that both lineages are genetically as strongly differentiated frommantoas other taxonomically well separated sibling species in this genus from each other, supporting a delineation ofbubastisandvogesiacaas independent species. Given the restricted and isolated range ofvogesiacaas well as the disjunct distribution ofbubastis,our findings have significant implication for future conservation efforts on these formerly cryptic species and highlight the need to investigate the genomic identity within species complexes.Supplementary InformationThe online version contains supplementary material available at 10.1007/s10592-023-01501-w.