A chiral CD-MEKC method, enantioselective for catechin and gallocatechin, was developed, validated and applied to the analysis of tea samples. The method was addressed to the fast and simultaneous quantitation of the most represented and biologically important green tea catechins and methylxanthines. The CD-MEKC was based on SDS as surfactant (90 mM) and hydroxypropyl-beta-CD (25 mM) as chiral selector, under acidic conditions (25 mM borate-phosphate buffer, pH 2.5). The method was first applied to study the thermal epimerisation of epi-structured catechins, (-)-epicatechin and epigallocatechin, to non-epi-structured (-)-catechin and (-)-gallocatechin. The latter compounds, being non-native molecules, were for the first time regarded as useful phytomarkers of tea samples subjected to thermal treatment. The proposed method was applied to the analysis of more than twenty tea samples of different geographical origins (China, Japan, Ceylon), having undergone different storage conditions and manufacturing processes. Finally, factor analysis was used to visualise the useful information contained in the data set, showing that it was possible to distinguish tea samples on the basis of their different contents of native and non-native catechins.