The contents of quercetin glycosides and neochlorogenic acid in fresh berries of Cornelian cherry and Common dogwood were assessed through LC–MS/MS analysis to determine chemical differentiation between two distant populations of each species. The aim of this study was to investigate the chemical variability of Cornus mas and Cornus sanguinea on the basis of the content of six selected phenolic compounds in fruit extracts. Fruits were sampled at the time of full ripening, mid-September, from two localities that differed in terms of orographic and environmental conditions. Fresh fruit extracts were analyzed by LC–MS/MS to determine the presence and contents of neochlorogenic acid, quercitrin, isoquercetin, hyperoside, rutoside and querciturone. While all of the tested compounds were detected in both species, their content was several times higher in C. sanguinea. Locality-dependent differences were tested by appropriate statistical tests, which confirmed that the contents of all compounds significantly differed in C. mas, whereas the content of only one compound differed in C. sanguinea. Differences between populations were also revealed by PCA analyses. Both species showed clear separation of populations based on the analyzed phenolic compounds. The results showed that a specific environment can significantly affect the contents of certain secondary metabolites, as in the case of C. mas, and/or that the synthesis of these compounds can be to a lesser extent influenced by external factors, as in the case of C. sanguinea.