Biodiversity is essential for maintaining ecosystem services and each species performs a particular function in an ecosystem. It constitutes a unique global heritage and its conservation and utilization is of immediate concern. The increasing loss of aquatic biodiversity globally has led the researchers to intensify their efforts to produce a census of all aquatic biodiversity and to modernize the taxonomy. It is not feasible to catalogue the vast diversity by traditional methods based on morphological description so the researchers adopt analytical molecular technologies as an alternative to fill the gaps in phylogeny. In this direction, DNA markers have revolutionized the analytical power necessary to explore the genetic diversity. The present article collates information on all types of molecular markers with their principles, important advantage and disadvantages with respect to aquatic biodiversity studies. Among them mitochondrial DNA markers are being used extensively in aquatic biodiversity and conservation studies particularly in tracking invasive species, detection of cryptic species and identification of various life history stages. Focus has been given on mtDNA based markers such as DNA Barcoding, mini-DNA Barcoding and environmental DNA (eDNA) based meta-DNA Barcoding technologies useful for aquatic biodiversity studies.