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. These molecular markers combined with new statistical developments have revolutionized the analytical power, necessary to explore the genetic diversity. 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, SNP or RAPD) are now being used in fisheries and aquaculture. These markers provide various scientific observations which have importance in aquaculture practice recently such as: 1) Species Identification 2) Genetic variation and population structure study in natural populations 3) Comparison between wild and hatchery populations 4) Assessment of demographic bottleneck in natural population 5) Propagation assisted rehabilitation programmes. In this review article, we have concentrated on the basics of molecular genetics, overview of commonly used markers and their application along with their limitations (major classes of markers) in fisheries and aquaculture studies.
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