Abstract
The speckled shrimp Metapenaeus monoceros is a commercially important penaeid shrimp in the Indo‐West Pacific region including Bangladesh. Phylogenetics of penaeid shrimps is still a debatable issue, and molecular variation within the species is large. This study focused on the phylogeography of M. monoceros, including an assessment of the phylogenetic relationships among seven other Metapenaeus species by assessing sequence variation in three mitochondrial markers, the cytochrome oxidase subunit 1 (CO1), control region (CR) and 16S rRNA (16S). In addition, the mitochondrial variation along the Bangladesh coastline was analysed. The mitochondrial variation has a clear geographical pattern with two distinct evolutionary lineages, one found in the western Indian Ocean and the Mediterranean Sea and the second in the eastern Indian Ocean. A phylogenetic analysis of Metapenaeus based on the three markers revealed polyphyletic relationships within the genus and that the taxonomy needs revision. The mtDNA variation in Metapenaeus monoceros in Bangladesh presents a single population (AMOVA, F ST and Φ ST p > .05), which started to expand around 467 (CI: 186–753) kyr ago, and is characterized by a large number of closely related haplotypes. The study could be used to improve the management and conservation of the shrimp fishery in the region.