The study focused on the determination and comparison of the total phenolic contents in the seeds, skin, and flesh of two grape hybrids, namely Isabella (Vitis vinifera × Vitis labrusca) and Othello (Vitis labrusca × Vitis riparia × Vitis vinifera) grown in Debrecen, Hungary, as well as their anthocyanin compositions in the skin fraction by the vortex-mixing and ultrasonic-cleaning extraction procedures. The impacts of two different experimental designing methods on the profile of phenolic and individual anthocyanin compounds in analyzed extracts were evaluated. The highest concentration of phenolics determined by Folin-Ciocalteu assay was found in the grape seeds, followed by skins and flesh. The predominant individual anthocyanins in all examined grape skin extracts were malvidin-3-O-glucoside, identified by the reversed-phase high-performance liquid chromatography (HPLC). The results showed that the quantification of total phenols and anthocyanin compositions is dependent on the genome of grape cultivars.