Isoflavones are the main phenolic compounds of soy influencing its biological activity; however, their amount may differ significantly. In this work, the content of isoflavones in various soy taxa was determined using the high performance liquid chromatography with diode array detection (HPLC-DAD) and mass spectrometry (MS) technique. Moreover, the total phenolic content (TPC) and the antioxidant activity of the investigated soybean seeds were analysed using UV–vis spectrophotometric assays. Daidzin (daidzein 7-O-glucoside), malonyldaidzin, genistin (genistein 7-O-glucoside), and malonylgenistin were the dominant isoflavones present in all soybeans seeds. High fluctuations of their content were observed. The cultivars Caloria, Safir, and Brovallia were the richest sources of isoflavones; with total values of 3813, 3198, and 4030μg/g, respectively. All tested soybeans exhibited significant antioxidant activity; however, no correlation between the amount of isoflavones and TPC vs. antioxidant activity was noted.