Puntius is a genus belonging to the family Cyprinidae; the most widely distributed freshwater fish all over the world. There are confusions in the taxonomic status of this genus whereby the classification of this genus is based solely on the morphological characteristics. Thus, the present study highlighted the phylogenetic relationships among common cyprinids found in Peninsular Malaysia. Fifty samples of Puntius were collected from different locations in Peninsular Malaysia, namely Sungai Pahang, Sungai Perak, Banting (Selangor) and Terengganu. Our data set was complemented by cytb and Rag2 sequences of all of Puntius genus and other endemic genera of cyprinidae from GenBank, The intrageneric K2P distance for mitochondrial and nucleus genes, revealed there might be more than one real homogenous involved in this complex genus. The phylogenetic tree with mitochondrial and nucleus gene revealed that Puntius is paraphyletic genus because different species of Puntius did not cluster to each other.

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