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Freshwater fish biodiversity is a precious natural asset in terms of economic, cultural and scientific interest. And yet, the inland freshwater ecosystem in Malaysia is declining at a far greater rate than terrestrial ecosystems in the tropics. What happened, and what is being done to address the crisis? This paper extracts findings from the latest literature and explores overarching issues pertaining to freshwater ichthyology in Malaysia. Various schools of thought on biogeography and some basic data are first discussed to characterise Malaysia’s fish species distribution and diversity. Subsequently, fish research and conservation concerns are explicitly raised and discussed to reveal concerns affecting the research movement and freshwater habitat quality. It is hoped that this short review provides vital information to consolidate and drive effective national policies and programs for safeguarding the country’s freshwater fish biodiversity.