The discovery of an adaptive immune system especially in archae and bacteria, CRISPR/Cas has revolutionized the field of agriculture and served as a potential gene editing tool, producing great excitement to the molecular scientists for the improved genetic manipulations. CRISPR/Cas9 is a RNA guided endonuclease which is popular among its predecessors ZFN and TALEN’s. The utilities of CRISPR from its predecessors is the use of short RNA fragments to locate target and breaking the double strands which avoids the need of protein engineering, thus allowing time efficiency measure for gene editing. It is a simple, flexible and highly efficient programmable DNA cleavage system that can be modified for widespread applications like knocking out the genes, controlling transcription, modifying epigenomes, controlling genome-wide screens, modifying genes for disease and stress tolerance and imaging chromosomes. However, gene cargo delivery system, off target cutting and issues on the safety of living organisms imposes major challenge to this system. Several attempts have been done to rectify these challenges; using sgRNA design software, cas9 nickases and other mutants. Thus, further addressing these challenges may open the avenue for CRISPR/cas9 for addressing the agriculture related problems.