The Mekong River Basin represents a global hotspot of aquatic biodiversity second only to the Amazon River in terms of total fish species richness. Our study focuses on phylogeny of freshwater fish in Vietnamese Mekong. Freshwater fish species were sampling at 7 Provinces along Hau and Tien rivers. Morphologically, 11 species have been identified. Phylogenetic trees were constructed based on 16S and CO1 gene of mitochondrial DNA using Maximum Parsimony, Maximum Likelihood and Bayesian Inference approaches.

The 16S phylogram performed similar phylogenetic relationships of CO1 phylogeny, excluding difference in position of Coilia species (family Engraulidae) and Acantopsis (family Cobotidae). Our results corroborate the monophyletic status at genus level (includes: Pangasius, Ompok, Acantopis, Trichopodus, Glossogobius, Coilia, Acantopsis and Cynoglossus). Moreover, sequence differences have been found between G. circumspectus and G. olivaceuin in C01, while they are identical in 16S gene. Current data can be used as data sources for the study of biodiversity and management of fisheries resources in the Mekong Delta in Vietnam.