The chemical analysis of tartaric acid (TA) and syringic acid (SA), as grape product markers in ancient ceramic vessels from the sites of Manduria and Torre di Satriano (southern Italy), was successfully performed. Firstly, the fragmentation behaviour of TA and SA as deprotonated molecules, [M-H](-), obtained by collision-induced dissociation, was investigated. Then, reversed-phase liquid chromatography (RPLC) with electrospray ionization (ESI) in negative ion mode, using a quadrupole linear ion trap in multiple reaction monitoring (MRM), was employed. A binary mobile phase composed of water-acetonitrile with 0.1% (v/v) acetic acid enabled the optimum ESI efficiency of SA, greatly improving its identification when it occurs in trace amounts. Chemical analysis of ancient pottery fragments is a valid method for establishing the existence of preserved organic residues, which is valuable new evidence for the culture and customs of ancient populations, in this case those of southern Italy. The proposed RPLC-ESI-MRM method allowed a systematic investigation of ceramic fragments of both archaeological sites, thus providing positive evidence for the presence of TA and SA as grape product markers in storage vessels dating back to the ninth to third centuries BC.