In this review, we have discussed the basic principles, uses, advantages and disadvantages of the most widely used molecular markers for genetic diversity studies, genetic mapping, marker-trait association studies and marker assisted selection programs. It is theoretically possible to observe and exploit genetic variation in the entire genome with different molecular markers. Most common genetic markers include allozymes, mitochondrial DNA, RFLP, RAPD, AFLP, microsatellite and SNP. Hence, the development and use of molecular markers for the detection and exploitation of DNA polymorphism is one of the most significant developments in the field of molecular genetics and medical sciences.