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The assemblage patterns of larval fishes from three neighboring tributaries viz., Songkram, Gam and Mun of the Mekong River in Thailand were investigated between August 2009 and June 2010. These rivers interact with their floodplains, which are important spawning and nursery grounds for the Mekong fishes. There is no dam along the Songkram River; meanwhile the Gam River has several irrigation dams with a fish ladder at each dam site and the Mun River has a hydropower dam with a fish ladder and sluice gates that are opened during the wet season each year. A total of 97 fish species were collected from the study sites. Assemblage of Gam River was dominated by larvae of resident, black fish species. Assemblage of Mun River during sluice gate opening scheme was similar to that of Songkram River during wet season. Assemblage during flood period of Songkhram River showed the most diversity and abundance of migratory, white fish larvae. Conservation of integrity of the floodplain-river system of Songkhram River is among the crucial strategies for sustaining fish diversity and fisheries in the Lower Mekong River Basin.