Field experiments showed that the co-cultivation of pearl mussels and fishes formed a new biocoene composed of filamentous algae, protozoa, porifera,coelenterate and bryozoa on the rope, net, floats and shells. A new biocoene formed in the water 20-40 cm under the surface. The investigation showed increases of algae species and groups, which represented an increase of biodiversity. The algae fond of high nitrogen and phosphorus decreased, while those fond of high iron, magnesium, zinc and low nitrogen and phosphorus increased. It effectively reduced nitrogen, phosphorus, chemical oxygen demand and biochemical oxygen demand in the water by 67.3%, 73.2%, 38.1% and 15.5%, respectively, from May to September when the water eutrophication was developing. This changed the transparency and nutrition levels of the water, and meanwhile the products, such as pearl, shellfish meat and shell, etc. could be caught. This is an economical and effective way to control water eutrophication.