A molecular marker is a site of heterozygosity for some type of silent DNA variation not associated with any measurable phenotypic variation. Such a "DNA locus," when heterozygous, can be used in mapping analysis just as a conventional heterozygous allele pair can be used. Because molecular markers can be easily detected and are so numerous in a genome, when they are mapped by linkage analysis, they fill the voids between genes of known phenotype. Note that, in mapping, the biological significance of the DNA marker is not important in itself; the heterozygous site is merely a convenient reference point that will be useful in finding one's way around the chromosomes. Genetic variation in a species enhances the capability of organism to adapt to changing environment and is necessary for survival of the species. Genetic variation arises between individuals leading to differentiation at the level of population, species and higher order taxonomic groups. The genetic diversity data has varied application in research on evolution, conservation and management of natural resources and genetic improvement programmes etc. Development of molecular genetic markers has powerful ability to detect genetic studies of individuals, populations or species. Molecular markers and their statistical analysis revolutionized the analytical power, necessary to explore the genetic diversity. Various molecular markers, protein or DNA (mt-DNA or nuclear DNA such as microsatellites, Single Nucleotide polyphosphate or Randomly Amplified Polymorphic DNA) are now being used in fisheries and aquaculture for species identification, genetic variation and population structure study in natural populations, comparison between wild and hatchery, assessment of demographic bottleneck in natural population and designing propagation assisted rehabilitation programmes.