The skill of inactivating, deleting or replacing genes in organisms helps us to understand the important biological processes that sustain life. Genome editing in plants and other species with the aid of site-specific nucleases has been accomplished with success. Varieties obtained by genome editing in plant breeding have less regulatory procedures as compared to GM crops. The most influential strategies for targeted genome engineering are meganucleases, ZFNs, TALENs and CRISPR/Cas. Naturally, cells have endogenous repair mechanisms, viz. NHEJ and HDR, for DNA double-stranded breakage, which is used in genome editing. The rapid development of genome editing in the field of agriculture will help to improve yield and to gain resistance against various biotic and abiotic stresses. We have summarized breakthroughs that extended the potential of genome editing methods from basics to the applied part for crop improvement, which will help to tackle emerging problems in agriculture and food security.