The nature act like a large “bio-laboratory” comprising of plants, algae, fungi, yeast etc. which are composed of biomolecules. These naturally occurring biomolecules have been identified to play an active role in the formation of nanoparticles with distinct shapes and sizes thereby acting as a driving force for the designing of greener, safe and environmentally benign protocols for the synthesis of nanoparticles. The present review targets the comparative biogenic synthesis and mechanisms of nanoparticles using algae and waste materials (agro waste in the presence of biomolecules. The use of waste materials not only reduces the cost of synthesis but also minimizes the need of using hazardous chemicals and stimulates ‘green synthesis’. It also focuses on the computational aspects of binding of biomolecules to nanoparticles and some of the applications of the biosynthesized nanoparticles in biomedical, catalysis and biosensors fields.