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Morphological traits in Haliotidae may be highly variable and not consistently diagnostic for species identification, highlighting the need for an integrative approach to the taxonomy of the family, including genetic data. Four species of the genus Haliotis are currently reported for the Mediterranean Sea and the neighboring Atlantic Ocean: Haliotis tuberculata, the common European abalone with the widest Atlanto-Mediterranean range; Haliotis mykonosensis, from the Aegean, the Tyrrhenian, and the Adriatic; Haliotis stomatiaeformis, from Malta, Lampedusa, and southeastern Sicily; and the Lessepsian Haliotis pustulata, only known on the basis of few samples from the Levant. However, their taxonomic status still relies only on shell morphology. Here, sequences of two fragments of the mitochondrial molecular marker COI were obtained from 84 abalone specimens collected in the Mediterranean Sea and the neighboring Atlantic and analyzed in order to provide for the first time a genetic framework for species delimitation. This study’s results prove that H. mykonosensis is genetically identical to H. tuberculata, whereas H. stomatiaeformis is a distinct species, endemic to a restricted area of the southern Mediterranean Sea. Finally, Haliotis tuberculata coccinea from Macaronesia may deserve its status as a subspecies of H. tuberculata, with genetic signature of a limited gene flow found in specimens of the nominal subspecies (H. t. tuberculata) in both the Atlantic and the Mediterranean Sea.