The use of molecular markers, revealing polymorphism at the DNA level, has been playing an increasing part in plant molecular biotechnology and their genetic studies. There are three different types of markers viz. morphological, biochemical and DNA based molecular markers. These DNA based markers are differentiating in two types 1. Non PCR based (RFLP) and 2. PCR based markers (RAPD, AFLP, SSR, SNP etc.). Amongst others, the microsatellite DNA marker is one of the most widely used marker due to its easy use by simple PCR, followed by a denaturing gel electrophoresis. SNP (Single Nucleotide Polymorphism) is nowadays is the one which is used mainly. In this review, we are going to discuss about the biochemical and molecular markers which are recently developed, the important characteristics of molecular markers their advantages, disadvantages and the applications of these markers in comparison with other markers types.