Abstract: The research results of nitrogen biotransformation and its relative microorganism in aquaculture waters are summarized. It is pointed out that nitrogen cycle in aquaculture waters mainly originates from the formulated feeds and the inorganic or organic fertilizers, which form complex dynamic balances through continuously transferring and transformation under interaction of organism and in-organism. Microorganisms play a key role in this cycle, the sediment-water interface is an important place of the mineralization of organic matter and regeneration of nutrition. Finally, some regulating practices are given that can influence the nitrogen cycle in the course of fish culture.