Fenneropenaeus indicus is a commercially important penaeid shrimp for capture fisheries and aquaculture in the Indo-Pacific region. Phylogeny of penaeid shrimps is still a debatable issue and molecular variation within the species is large. This study focuses on phylogeography of F. indicus along with four other species of the genus. Sequence variation of the mitochondrial COI gene of wild F. indicus sampled from Bangladesh was analysed. The phylogenetic of Fenneropenaeus genus was studied by analysing COI and 16S rRNA genes applying Bayesian and Maximum likelihood methods. Genetic diversity of Bangladesh F. indicus recognizes it as a single population which passed through a bottleneck in 41.5-77.1 thousand years ago. Although a high variation is observed in number of haplotypes, the genealogical relationships are shallow and the overall variation is much less than that was reported for Sri Lanka. Comparison of population throughout the Indo-Pacific region shows a clear geographical pattern with distinct evolutionary lineages. A phylogeny shows that these lineages within F. indicus even predate the speciation of other Fenneropenaeus species. Sri Lankan population clusters with F. merguensis, and Australian one with F. peniciliatus and F. silasi. Thus, F. indicus shows polyphyletic relationships among Fenneropenaeus genus and the taxonomy needs to be reevaluated. The study of the population biology of F. indicus will be helpful both for management and conservation of diversity.