In this work two Iraqi plants (Datura Stramonium and atropa belladonna) has been studied. Extraction and isolation of atropine from these plants were investigated. The extraction was done using methanol as a solvent using soxlet apparatus. Atropine was identified by melting point which was found to be (113-116 o C) in Atropa belladonna and (114-118oC) in Datura stramonium which was in good agreement to the standard value (114-116C0). F.T.IR, UV-Vis, HPLC and TLC achieve the presence of atropine. HPLC analysis shows New Flavonoid compounds in the two plants in small concentrations. Rutin and Qurecetin were separated in Datura stramonium while Catechin was found in Atropa belladonna. TLC also confirmed the presence of these compounds by comparison the Rf values of each extracted compounds with the standard Rf values. Biological activity was determined using disc diffusion method with two strain of pathogenic microorganisms viz., Staph.aureus and E.coli. These results obtained using different water extract concentrations (5µg/ml, 10µg/ml, 15µg/ml, and 20µg/ml) showed measurable activity against the two types of bacteria.