Puntius spp. (Cypriniformes: Cyprinidae), commonly known as silver barb fish, is widely distributed in Asian tropics. There are confusions in the taxonomic status of this genus where some authors have recently changed some of the Puntius species name under the genus Barbodes. The validity of changing this genus name remains unanswered. Since the current taxonomic classification is solely based on morphological characters, many species in this genus could probably be subdivided into several distinct groups. Thus, the present study highlighted the phylogenetic relationships among ten species of Puntius inferred from both mitochondrial and nuclear genes by using DNA sequences from the Cytochrome b (857 bp), Cytochrome oxidase 1 (501 bp), and recombination activating gene 2 (860 bp). Samples were collected from five different locations in Peninsular Malaysia, namely Sungai Pahang, Sungai Perak, Selangor, Johore and Terengganu. Phylogenetic reconstructions using maximum parsimony, maximum likelihood, and Bayesian analyses for all genes retrieved similar clades, only branching order within these clades varied slightly between trees. The intrageneric distance for each mitochondrial and nuclear gene suggesting that there might be more than one real homogenous involved in this complex genus of Puntius.

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