The aim of this work was to assess whether the characteristic polyphenol traits of cherry biotypes persisted in thermally processed cherry products, such as jam. Thus, the RP-HPLC-diode array detector profiles of both colorless polyphenols and anthocyanins from three cherry varieties (two sweet and one tart cherry) were compared with those of low-sugar jam sourced from the same cultivars. Individual components were characterized by mass spectrometry. The total phenolic and total anthocyanin content as well as the radical scavenging potential (residual 75-91, 88-91 and 73-75%, respectively) were only slightly reduced by deep thermal treatments. Apart from the interconversion among the isomers of chlorogenic acid, the profile of both colorless polyphenols and anthocyanins substantially survived the jam manufacturing under conventional temperature-time regimen (80°C, 1h). The species- and cultivar-specific polyphenol molecular asset, especially the anthocyanin pattern, has potential to be monitored for traceability purpose, aimed to the varietal assessment of cherry biotypes used for producing jam.