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Blackberry wine is a natural source of bioactive phenolic compounds that have profound antioxidant potential. The objectives of the present research were to assess the phenolic compounds and antioxidant activity of blackberry wines (BW), and to use the chemometric analysis to differentiate among the two groups of samples, i.e., conventional and organic. Fifteen BW samples were analyzed for their total polyphenol index, total polyphenols, total flavonoids, total tannins, total monomeric anthocyanins and antioxidant activity by the appropriate spectrophotometric methods. The concentrations of individual phenolic acids (gallic acid, chlorogenic acid, caffeic acid, p-coumaric acid and cinnamic acid) and trans-resveratrol were determined by high-performance liquid chromatography. A comparison between the two groups of investigated BW samples revealed a statistically significant difference in the concentration of caffeic acid and p-coumaric acid, both being higher in the organic BW samples. Furthermore, the results showed a series of statistically highly significant relationships between the analyzed constituents (caffeic acid and p-coumaric acid). The antioxidant activity of the investigated wines was proportional to the concentrations of bioactive phytochemicals.