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¹ Sher-e-Kashmir University of Agricultural Sciences and Technology, Faculty of Veterinary Sciences and Animal Husbandry, Division of Animal Biotechnology, Kashmir, India DOI : 10.4194/2459-1831-v1_1_05 Viewed : 14372 - Downloaded : 25439 Although aquaculture management becomes challenging because of overuse, pollution and human activities reduced resources and genetic variations, current developments in molecular technology and genome programs have created an enormous evidences to be used for the genetic advancement of aquaculture. Over the past decade, using molecular markers showed polymorphism at the DNA level and played rising role in aquaculture. The utility of DNA markers has certified the hastiness in the exploration of fish germplasm. Various molecular markers present and their differences in principles, methodologies and applications still need careful consideration in selecting more useful marker for the successful management of aquaculture. In addition to the basic principles, necessities, pros and cons of various markers, this review also discusses their usage in different aspects of aquaculture; we provide an overview of the potential of various techniques of functional genomics like expressed sequence tags (EST), microarrays and RNA sequencing in aquaculture. Keywords : Molecular markers, RFLP; RAPD, AFLP; microsatellites, SNP, mitochondrial DNA, microarray, RNA sequence, fisheries, aquaculture