A large number of plants produce secondary metabolites known as allelochemicals that are capable of inhibiting the germination of competitive species. This process is known as allelopathy and is mediated by several classes of chemicals, among which phenolic compounds are the most frequent. Thus, plant allelochemicals can be used to control weeds in agricultural systems. In the present work, we analyzed the phenolic profile and phytotoxic potential of different extracts (pure water or water: ethanol 50:50) from Scrophularia striata plants that were collected from two ecological regions in Iran (Pahleh and Lizan). The total polyphenolic content (TPC), as evaluated by the Folin-Ciocolteau method, ranged from 28.3 mg/g in the aqueous extract obtained from the Lizan ecotype to 39.6 mg/g in the hydroalcoholic extract obtained from the Pahleh ecotype. Moreover, HPLC analysis was aimed at determining the content of eight phenolic compounds, namely eugenol, rosmarinic acid, hesperetin, hesperedin, trans-ferulic acid, vanillin, and caffeic acid. According to the results, rosmarinic acid appeared to be the most abundant component. The phytotoxic activities of S. striata extracts were examined on the seed germination of a crop species, Lepidium sativum, and two weeds, Chenopodium album and Malva sylvestris. All extracts showed inhibitory effects on these species. The efficiency of these inhibitory effects depended on the type of plant species, origin, and concentration of extract. The highest phytotoxic activity was caused by approximately 1% concentration of extract. The most susceptible weed was M. sylvestris. The extracts that were obtained from the Pahleh ecotype, notably the hydroalcoholic ones, showed higher phytotoxicity against L. sativum, C. album and M. sylvestris. These results encourage further studies to support the use of S. striata as a source of bioherbicides.