The thesis deals with the investigation of primary and secondary metabolites in fruits of various berry species (Ribes rubrum L., Rubus idaeus L., Vaccinium corymbosum L. and V. myrtillus L.). We aimed to link the expressions of regulatory and structural genes, related phenylpropanoid/flavonoid enzyme activities and phenolic composition in differently colored berry fruits of the same species. Metabolites were analyzed with HPLC and HPLC-MS, gene expression with RT-qPCR and enzyme activities with radiographic TLC scan. The results indicate that fruit color of white vs. blue colored bilberry (Vaccinium myrtillus L.) and differently colored cultivars of red currant (Ribes rubrum L.) is predominantly affected by anthocyanin content in fruit skin. Phenolic profile remained similar regardless of fruit coloration. Suppressed anthocyanin biosynthesis in white-colored bilberry compared to more common blue hues of bilberry fruit, were primarily correlated with reduced gene expression of flavonoid 3-O-glycosyltransferase (FGT) and anthocyanidin synthase (ANS) and secondly, with reduced gene expression/enzyme activity of flavanone 3-hydroxylase (FHT). Lower total phenolic content of white bilberry fruit can be associated with an additional bottleneck within the phenylpropanoid pathway at an unknown step between phenylalanine ammonia lyase (PAL) and chalcone synthase (CHS). This could explain significant increase in relative levels of hydroxycinnamic acid derivatives in white bilberries. Similarly, pink-colored red currant cultivar 'Pink Champagne' was characterized by lower chalcone synthase/isomerase (CHS/CHI), FHT and dihydroflavonol 4-reductase (DFR) activity and ANS expression in comparison with 'Jonkheer van Tets' (standard red berries). Moreover, no FHT and DFR activities were detected in red currant 'Zitavia' cultivar, which bears white fruits. Primary and secondary metabolite contents changed during red currant fruit ripening, which coincided with different activities of predominant flavonoid enzymes. Additionally, it was established that thermal treatment of highbush blueberry (Vaccinium corymbosum L.) purees affected the stability of phenolics. Greatest effect of higher temperature treatment was detected in total anthocyanin levels, which were significantly decreased. Cultivation technique − tipping the young first-year canes of primocane raspberry (Rubus idaeus L.) significantly delayed fruit ripening; however, the results did not show any uniform effects on the content of anthocyanins and other phenolic groups.