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Despite the existence of various therapeutic approaches, diabetes mellitus and its complications have been an increasing burden of mortality and disability globally. Hence, it is necessary to evaluate the efficacy and safety of medicinal plants to support existing drugs in treating diabetes. Xanthones, the main secondary metabolites found in <i>Gentiana dinarica</i> and <i>Gentiana utriculosa</i>, display various biological activities. In in vitro cultured and particularly in genetically transformed <i>G. dinarica</i> and <i>G. utriculosa</i> roots, there is a higher content of xanthones. The aim of this study was to investigate and compare antidiabetic properties of secondary metabolites (extracts) prepared from these two <i>Gentiana</i> species, cultured in vitro and genetically transformed with those collected from nature. We compare HPLC secondary metabolite profiles and the content of the main extract compounds of <i>G. dinarica</i> and <i>G. utriculosa</i> methanol extracts with their ability to scavenge DPPH free radicals and inhibit intestinal α-glucosidase in vitro. Anti-hyperglycemic activity of selected extracts was tested further in vivo on glucose-loaded Wistar rats. Our findings reveal that the most prominent radical scavenging potential and potential to control the rise in glucose level, detected in xanthone-rich extracts, were in direct correlation with an accumulation of xanthones norswertianin and norswertianin-1-<i>O</i>-primeveroside in <i>G. dinarica</i> and decussatin and decussatin-1-<i>O</i>-primeveroside in <i>G. utriculosa</i>.