Molecular markers are indispensable tools for identifying a particular sequence of DNA in a pool of unknown DNA. Use of Molecular markers are generally based on naturally occurring DNA polymorphism, which forms the basis for designing strategies to exploit for various purposes such as species identification, genetic diagnostics, characterization  of  transformants, study  of  genome  organization, germplasm characterization  and phylogenic analysis. There are various types of markers viz. morphological, biochemical and DNA based molecular markers. The molecular markers are selected for their appropriate purpose on the basis of high level of accuracy and reproducibility. The main properties which helps in choosing the most reliable marker are: Genetic abundance, level of polymorphism, locus-specificity, co-dominancy, technical demands, operational costs and many more. The DNA based molecular markers are again divided in to two i.e. hybridization based and PCR based molecular markers. RFLP belongs to the first non PCR based techniques and PCR based technique includes RAPD and AFLP. In this review, we discuss about the molecular markers with their merits and demerits.