Research article JOURNAL OF TROPICAL BIOLOGY AND CONSERVATION 5 : 1 - 13, 2009 1 ABSTRACT. A study on the genetic variation of Barbonymus schwanenfeldii (Bleeker) populations from Malaysia was done using partial sequencing of cytochrome b mtDNA gene. Samples were collected from various localities in Peninsular Malaysia, Sarawak and Sabah, including the Indonesian (Kalimantan) type of B. schwanenfeldii from Kapit, Sarawak. Phylogenetic relationship inferred using neighbour joining, maximum likelihood and maximum parsimony methods generally divided samples into two major groups, consistent with their geographic origin: one widespread group consisted of B. schwanenfeldii (locally known as Lampam sungai) from Peninsular Malaysia while another particular group clustered B. schwanenfeldii (locally known as Tengadak) from Sarawak. Within the Peninsular Malaysia, our current data supported the validation of two main divisions: central and southern division (CS; consisting of Serting River, Muar River and Padang Piol, Jerantut, Pahang) and north west and north east division (NWE; consisting of Pulau Banding, Perak and Tasik Timah Tasoh, Perlis). The low distance values between haplotype sequences (0.00 to 1.01) and low Phylogeny and phylogeography of Barbonymus schwanenfeldii (Cyprinidae) from Malaysia inferred using partial cytochrome b mtDNA gene Kamarul Rahim KAMARUDIN 1,2 and Yuzine ESA 3 1 School of Biological Sciences, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand. 2 Department of Biotechnology, Kulliyyah of Science, International Islamic University Malaysia (IIUM), Jalan Istana, Bandar Indera Mahkota, 25200 Kuantan, Pahang, Malaysia. 3 Molecular Ecology Laboratory, Department of Zoology, Faculty of Resource Science and Technology, Universiti Malaysia Sarawak, 94300 Kota Samarahan, Sarawak, Malaysia. nucleotide diversity, P i (0.005) showed a very close genetic relationship between samples, enforcing their taxonomic validation as belonging to a single taxon. However, the low level of gene flow (N m = 0.07) and high population structuring (F st = 0.88) between Peninsular Malaysia and Sarawak could be correlated with the separation of Borneo Island from mainland Peninsular during last Pleistocene Epoch. INTRODUCTION The greatest diversity of freshwater fish is found in tropical South America, Africa and South East Asia (Helfman et al., 1997). The fish diversity of South East Asia area was once affected during the Pleistocene Epoch of the Neogene Period. The Pleistocene was characterized by multiple episodes of glaciation, which caused ice to advance and retreat approximately every 100,000 years beginning about 2 million years ago (Dott & Prothero, 1994). Biogeographically, Malaysia is situated in the Oriental region. Peninsular Malaysia, southern Thailand, southern Indo- China, Sumatra, Java and Borneo were once part of the submerged Sunda Shelf (Mohsin & Ambak, 1983). In recent times, Peninsular Malaysia is separated from Borneo by the South Keywords: Barbonymus schwanenfeldii , partial cytochrome b, population genetics.