Nanotechnology is the most developing branch of science, it is thought that application of nanotechnology in agriculture will make this sector sustainable and profitable, by reducing the use of fertilizers, pesticides and by enhancing the crop productivity. In other words we can say that application of nanotechnology in agriculture will increase food and nutritional security. However, the main issue related with the application of nanoparticles in agriculture is their toxicity. It is therefore recommended for research organizations to provide research funds to establish safety standards and to develop new techniques for the toxic free synthesis of nanoparticles. Indian council of agriculture research (ICAR) has started a programme to study the effect of nanotechnology in agriculture. The ICAR- nanotechnology scheme has major themes such as synthesis of nano-particles for agriculture use, diagnostic kits for easy and quick identification of disease and pests, nano agri-inputs for enhanced use efficiencies, precision water management, and stabilization of organic matter in soil, nano food systems and bio safety besides establishing the policy frame work. Green synthesis and microbial synthesis of nanomaterial for agriculture use is very important as they are naturally encapsulated with mother protein, therefore more stable and safer to biological systems. The review presents here discuss applications of nanoparticles in agriculture. This review also features out the potential hazardous effects of nanoparticles on microbes and environment.