We employed the COI sequences from specimens of top-shells to: (a) test the applicability of COI as a barcode marker for the trochid genus Gibbula s.l.; (b) provide a first taxonomically reliable data set of COI sequences useful for future studies; and (c) detect evidence of suspect intraspecific variability over a large geographical scale. We analysed a data set of 150 sequences from specimens morphologically ascribed to 17 putative species of Gibbula from the Mediterranean Sea and northeastern Atlantic, including the type species of 9 taxa traditionally considered as subgenera of Gibbula and representing over 50% of the roughly two dozen Mediterranean species, and also provided the DNA barcode for the endangered Maltese top-shell Gibbula nivosa. The analysis of the data set revealed that the COI is an effective barcode for the identification of the northeastern Atlantic top-shells, and also provides a tool to detect cryptic diversity.