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Applying molecular (AFLP and sequences of nuclear ribosomal ITS), karyological (relative genome size estimations and chromosome counts) and morphometric methods we explored the origin of Italian endemic Euphorbia gasparrinii. AFLP data inferred three phylogeographic groups corresponding to Balkan-Central European-northern Italian E. verrucosa, Italian E. gasparrinii and Iberian E. flavicoma. Genetic differentiation among the three species is weak, suggesting their relatively recent divergence. Karyological analyses revealed that populations of E. gasparrinii have 2n = 16 chromosomes, whereas the other two taxa have 2n = 14. This, with weak genetic differentiation and allopatric distribution, supports its recognition as an independent species, despite its weak morphological differentiation. Our study also revealed multiple autopolyploidization events within all three taxa. Contrary to the diploid Apennine populations, the single currently known Sicilian population of E. gasparrinii is tetraploid. It is critically endangered, as the Sicilian distribution has decreased significantly during the past century. Our study underlines the importance of southern European peninsulas as refugial areas during the Pleistocene and provides additional evidence that Mediterranean high mountain plants are suffering severe range contractions due to climate warming.