Frangula alnus and Peganum harmala populations growing in Saudi Arabia might be rich sources of natural compounds with important biological activities. A high performance liquid chromatography diode array revealed several polyphenols in the leaf extracts for the first time, including p -coumaric acid, rosmarinic acid, chlorogenic acid, ferulic acid, quercitrin, rutoside, quercetin and trifolin in F. alnus; and hydrocaffeic acid, protocatechuic acid, rosmarinic acid, caffeic acid and cynaroside in P. harmala. F. alnus and P. harmala showed strong antioxidant effects attributed to the polyphenolic composition of leaves and reduction of reactive oxygen species (ROS) accumulation. F. alnus and P. harmala leaf extracts showed cytotoxic effects against Jurkat, MCF-7, HeLa, and HT-29 cancer cells using MTT and flow cytometry assays. These activities were attributed to the polyphenolic composition of leaves including quercitrin, trifolin and cymaroside, as well as the activation of caspase family enzymes 2, 6, 8 and 9 in treated cancer cells compared to control. The current findings of this study include a novel comprehensive investigation on the polyphenol composition and anticancer effects of leaf extracts of F. alnus and P. harmala from natural populations in Saudi Arabia.