Boyeria irene and Boyeria cretensis are species of spotted dragonflies belonging to the ‘darner’ family, Aeshnidae. In 1991, Peters classified Boyeria from Crete as B. cretensis, based on adult morphological characters. In this study, we used molecular evidence to determine if indeed B. irene and B. cretensis are different species. DNA was sequenced from samples of B. irene (from France, Switzerland, Tunisia, Spain and Italy) and B. cretensis (from Crete). These species were recovered as two different clades with strong support. We conclude that B. irene and B. cretensis are different species, with evidence based on molecular and morphological differences. In addition, we present the first phylogenetic hypothesis for Boyeria for which we have sequenced all but three species. Lastly, we discuss different scenarios that may have led to the present-day distribution and speciation patterns of Mediterranean Boyeria.