An analytical protocol to identify the organic dyes in micro samples of painted pottery has been developed by three different techniques - High Performance Liquid Chromatography, Gas Chromatography coupled with Mass Spectrometry, and Direct Exposure Mass Spectrometry. Results are presented for reference materials and red samples from a clay vessel found in Taranto, Italy in a tomb of the 2nd - 3rd century B.C.. This analytical procedure allowed the authors to identify two Rubia species molecular markers, alizarin and purpurin. On the basis of the identification of these chromophores within their historical and geographical context, the use of madder (Rubia tinctorum) can be concluded for one sample.