The principle, the application conditions and the localization of biomanipulation and non-traditional biomanipulation were analyzed. The countermeasure of biomanipulation of water quality was carried out in Lake Chaohu. The results were; The key mechanism of biomanipulation is to use zooplankton to control phytoplankton, but zooplankton can not effectively control filar alga and cyanobacterial blooms;generally, there are not plentiful zooplankton in large-scale shallow lakes, so the stress of zooplankton on alga is usually littler. Moreover, the alga fed by zooplankton grow more rapidly than before. Besides, zooplankton is the impor-cant energy path between alga and fishes which can not directly feed on alga, so zooplankton should not be protected excessively.However, The main content of non-traditional biomanipulation is that cyanobacterial blooms was controlled by silver carp and big-head. Silver carp and bighead are able to control cyanobacterial blooms only in threshold biomass, but can not control all kind of alga and reduce N and P. The countermeasure to deal with eutrophication in local area should be that the measurement such as non-traditional biomanipulation, restoration of aquatic vegetation and renewedly construct of ecosystem were combined into a unite which have the function of controlling cyanobacterial blooms to produce fishes and reducing N and P to depurate pollution water.