Fourteen compounds belonging to different chemical classes were characterized in the roots and fruits extracts from Berberis libanotica, using the same HPLC-DAD-MS method. Thirteen were reported, for the first time, from the fruits whereas the roots contained mostly alkaloids of which 3 out of 5 are reported for the first time. Their structures were established on the basis of MS data as gallic acid (1), chlorogenic acid (2), delphinidin (3), oxyacanthine (4), rutin (5), hyperoside (6), berbamine (7), isoquercitrin (8), quercitrin (9), jatrorrhizine (10), palmatine (11), berberine (12), quercetin (13) and luteolin (14). Extracts containing compounds 4 and 7 showed significant cytotoxicity against the HT29 cell line with an IC50 of 12.2-26.1 μg/mL. Fruits extracts, due mostly to compounds 1 and 2, showed potent antioxidant activities with an EC50 of 0.0025-0.019 mg/mL.