The knowledge of the genetic architecture of closely related species and/or populations of a single species can be very useful to shed light on the processes that led to their current distributions. The present study provides a preliminary evaluation of the conservation status of the populations of Cryptotaenia thomasii, a very narrow endemic species occurring in southern Italy. Previous studies showed that C. thomasii was phylogenetically closely related to C. flahaultii, endemic species of Caucasus, and to evaluate its conservation status and the genetic variability of plant species the internal transcribed spacers (ITSs) of nuclear ribosomal DNA were sequenced and the SNPs were analyzed. The restriction analysis of nrDNA with the restriction enzymes allowed to detect the presence of two single mutations (SNPs) among the sequences of two species. Our molecular analysis pointed out that C. thomasii and C. flahaultii, in spite of their geographical disjunction, show a sign of an ancient contact as an extreme case of geographical disjunction Italian-Caucasus. From the evolutionary history of the species and its distribution pattern one can reconstruct a possible scenario with some hypotheses that explain the hypothetical ancestral area where the two species were in contact. We speculate the two species may have originated from fragmentation of a common ancestor widespread in the Western Palearctic zone and have survived in two separated refuge areas limited by important mountain systems. This hypothesis is supported by our molecular analysis, in fact, the analysis of SNPs showed that some C. thomasii populations retain the signs of an ancient link with C. flahaultii.