Among the methods that have been developed for anthocyanin characterization, matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS) offers several analytical advantages in terms of speed, minimal sample handling, specificity, and reliability, without requiring any previous chromatographic separation. This study used MALDI-TOF MS to profile the anthocyanins from the berry skins of 23 red grape varieties clustered as (i) authentic Vitis vinifera grapes, (ii) American hybrid cultivars, and (iii) Casavecchia cultivars, previously characterized as functional crosses of V. vinifera with nondefined hybrid grapevines. Anthocyanin profiling demonstrated evidence of several varietal traits that enabled the differentiation of authentic V. vinifera from hybrid cultivars on a molecular basis. In particular, acyl 3,5-O-diglucoside anthocyanins were established as easily monitored molecular markers of the hybrid varieties. It was also demonstrated that MALDI-post source decay MS is a powerful tool to differentiate isobaric 3,5-O-diglucosides and their derivatives, which prevail in hybrid cultivars, from acylated 3-O-glucoside anthocyanins.