Recently, enamel peptides revealed their critical role in sex classification of old skeletal remains. In particular, the presence of protein AMELY (amelogenin isoform Y) within the enamel dental tissue is restricted to the male sex only, while AMELX (isoform X) can be found in both sexes. AMELY can be easily detected through peptide SM(ox)IRPPY by means of LC-MS/MS and retrieved from ion chromatograms (exact mass [M+2H]+2 440.2233 m/z). In this paper, we exploited the dimorphic features of the amelogenin protein to unravel the sex of the so-called ‘Lovers of Modena’, two Late Antique individuals whose skeletons were intentionally buried hand-in-hand.