Accurate species delimitations are essential for establishing efficient conservation programs. Gortyna borelii (Noctuidae) is a threatened and protected moth, with a widespread, but localised in a range of meadows, forest clearings and edges in Europe. Larvae are internal feeders on a limited number of Peucedanum species, that are heavily impacted by intensive mowing regimes. Preliminary DNA barcode data from a few individuals showed a deep mitochondrial split in France suggesting a possible cryptic species complex. We DNA barcoded an additional 43 individuals sampled across France that confirmed the existence of two BINs, with a genetic divergence of 2.79%, one in Southeastern France (Maritime Alps) and Corsica and another in Western, central France and Eastern Pyrenees. RADseq data (9961 SNPs) from 34 individuals confirmed the existence of two clades but also revealed a substructure in five populations in France. The estimation of population genetic indices such as genetic diversity and inbreeding coefficient enabled us to assess the genetic status of these populations. This new insight into the genetic composition of G. borelii must be integrated into the conservation strategies to save this flagship species from extinction.