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In this study, the biosynthesis of iron (Fe), copper (Cu) and silver (Ag) nanoparticles was aimed using aqueous extracts of Polygonum cognatum (P. cognatum) and Tragopogon porrifolius (T. porrifolius). The synthesized nanoparticles were characterized using UV/Vis spectroscopy, fourier transform infrared spectroscopy (FTIR) and dynamic light scattering technique (DLS). The antibacterial activity of the nanoparticles was analyzed against well-known pathogens Klebsiella pneumonia, Pseudomonas aeruginosa, Enterococcus faecalis and Staphylococcus aureus. In addition, the anti-fungal activity of the nanoparticles against Candida albicans and Candida utilis strains was evaluated. The obtained results showed that the synthesized nanoparticles have a moderate antimicrobial effect.