Hypericum species are known for their ability to produce multiple classes of secondary metabolite and in this article the possible health-promoting role of H. empetrifolium and H. lydium have been evaluated combining in vitro and in silico approaches. H. empetrifolium and H. lydium extracts were obtained using different solvents (ethyl acetate, aceton, aceton/water, and water) and the composition was compared using NMR and LC–MS based approaches. Myricetin-3-O-glucoside, Kaemempferol -3-O-glucoside, and hyperopliphylirrin were present only in H. empetrifolium. Rutin, quercetin-3-O-rhamnoside ant the triterpenoids oleanolic and ursolic acid were only detected in H. lydium. To establish a possible role against degenerative diseases antioxidant, antiradical activities of the extracts were studied and H. empetrifolium acetone/water and water extracts were the more active regarding these effects. The extracts were also evaluated for the inhibition of key-enzymes involved in degenerative diseases namely cholinesterase and tyrosinase for CNS-related pathologies and amylase for metabolic-related diseases. Significant inhibition of acetylcholinesterase was observed for the extracts obtained with lipophilic solvents. The extracts were also studied for their possible antiproliferative activity on cell lines including tumor (DU-145, A549, and MCF-7) and non-tumoral cells (HEK-293) revealing moderate activities. H. lydium ethyl acetate showed late apoptotic (17.5%) and necrotic (46.6%) effects in the Annexin V/PI assay. Molecular docking was used to establish possible interaction of identified compounds with target enzymes and a good interaction between rutin and tyrosinase, myricetin-7-O-glucoside and amylase, was reported. In conclusion, Hypericum empetrifolium and H. lydium thanks to their complex pattern of phytoconstituents and thanks to their significant antioxidant effects as well as with the ability to act on some key-target enzymes involved in degenerative diseases can be considered a good vegetal source for the preparation of nutraceuticals and food supplements useful as health-promoting products against oxidative stress-related diseases such as diabetes, cancer, and Alzheimer's disease.