Recent developments in the biosynthesis of nanomaterials have demonstrated the important role of biological systems and microorganisms in nanoscience and nanotechnology. These organisms show a unique potential in environmentally friendly production and accumulation of nanoparticles with different shapes and sizes. Therefore, researchers in the field of nanoparticle synthesis are focusing their attention to biological systems. In order to obtain different applied chemical compositions, controlled monodispersity, desired morphologies (e.g., amorphous, spherical, needles, crystalline, triangular, and hexagonal), and interested particle size, they have investigated the biological mechanism and enzymatic process of nanoparticle production. In this review, most of these organisms used in nanoparticle synthesis are shown.