Many species of the subgenus Agrodiaetus have dotlike distribution ranges, and the delimitation of the majority of species is only possible on the basis of chromosomal and/or molecular data. In our research, we used a combination of chromosomal and molecular mitochondrial and nuclear markers to analyse the taxonomic identity and to study the phylogeographic history of an enigmatic Agrodiaetus population from South Poland. We discovered this population to be chromosomally and genetically indistinguishable from the widely distributed West Palaearctic species Polyommatus ripartii (Freyer, 1830). Moreover, this population was found to be genetically homogenous and to share the single identified COI+COII haplotype with populations from remote localities in Spain, Bulgaria and Ukraine. Coalescence-based dating with COI+COII marker estimated that the Polish population originated most likely 10 600–14 300 years ago. This estimation corresponds well to the age (11 700–12 000 years) of palaeontological remnant of Onobrychis arenaria, a food plant of P. ripartii, found in Poland. Generally, the data obtained support the hypotheses that (1) the common ancestor of the Central European populations originated in a refugium in the North Balkan, (2) after the last glacial maximum, this ancestor became broadly distributed in Europe and (3) the Nida population in Poland represents a relict of this ancient distribution.