The climatic history and complex geological of Southeast Asia have been hypothesized to determine the most important aspects of the current phylogeographical structure and distribution of biodiversity throughout the region. Numerous studies have been conducted to test this theory. However, the results have been varied and uncertain. Therefore, for better understanding of the effects, genetic pattern of the tire track eel, Mastacembelus favus, an obligate tropical freshwater fish is investigated. Two hundred sixty two samples were collected from eight river drainages encompassing its native range (Thailand, Lao PDR, Cambodia, Vietnam and Peninsular Malaysia) to evaluate the phylogeography, historical demography and species distribution by using partial cytochrome b gene. Strong genetic discontinuities were found between Lower and Middle Mekong populations suggesting a historical dissected drainage system between these two sections or species dispersal might have been accomplished via different colonisation routes. The widespread haplogroup is
signature of population expansion via an extended Pleistocene drainage network, Paleo-Chao Phraya River. Further studies on a finer sampling scale, more robust analyses and additional markers i.e microsatellites as well as a broader scope of study is in progress.