10.22376/ijpbs.2019.10.1.p1-12 Volume 10 Issue 4 2019 (October-December) The giant black tiger shrimp, lessThan i greaterThan Penaeus monodon lessThan /i greaterThan (Fabricius, 1798) is one of the most widely captured and cultured marine shrimp species and has a huge global economic impact. The last three decades, shrimp aquaculture has been threatened by various major virus outbreaks, mainly white spot syndrome virus. Therefore, evaluation of genetic diversity, as well as population genetic differentiation is required to identify overexploited regions of high-quality pond-reared lessThan i greaterThan P. monodon lessThan /i greaterThan . In this study, the population genetic diversity of lessThan i greaterThan P. monodon lessThan /i greaterThan was determined by the molecular data of the mitochondrial control region (mt D-Loop) and the 16SrRNA gene. The mitochondrial DNA (mtDNA) regions were highly AT-rich and a very high level of genetic diversity was observed. The diversity of 16SrRNA haplotypes was (0.963 ± 0.023), and the diversity of D-Loop haplotypes was (0.972 ± 0.017). The mitochondrial control region (D-Loop) was highly polymorphic and should be the potential markers for intraspecific population diversity study of lessThan i greaterThan P. monodon lessThan /i greaterThan . The 16SrRNA would be the best marker for phylogenetic studies in lessThan i greaterThan P. monodon lessThan /i greaterThan . Linkage disequilibrium analysis revealed that the increment of rare mutations and haplotypes. This study has a great significance to maintain high-quality pond-reared stock diversity, and also in accomplishing selective breeding. DEBABRATA MONDAL AND NRIPENDRANATH MANDAL Cultured Penaeus monodon, haplotype, mitochondrial DNA, genetic diversity, linkage disequilibrium, phylogenetics 51-68