Abstract. The application of 13 C and 15 N labeled phytoplankton makes it possible to directly follow the pathway and transfer of food source (cyanobacteria) into consumers (aquatic organisms), in contrast to past studies where only changes in compositions of chlorophyll-a, clearity, and nutrients were taken as the evidence for these processes. To evaluate the effect of biocontrol by aquatic organisms (aquatic plants; Iris pseudoacorus, filter feeder bivalve; Sinanodonta arcaeformis, and Unio douglasiae, macroinvertebrate; Caridina denticulate, carnivore fish; Pseudobagrus fulvidraco, Odontobutis platycephala, planktivore fish; Pseudorasbora parv, and omnivore fish; Misgurmus anguillicaudatus) on large toxigenic cyanobacteria bloom (Microcystis aeruginosa) in the freshwater ecosystem, we conducted a biomanipulation test on in situ ponds using dual stable isotope tracers ( 13 C and 15 N). As a filter feeding bivalve, S. arcaeformis could incorporate more toxic cyanobacteria cells than U. douglasiae, demonstrating its larger detoxification capacity. Also, macroinvertebrate (C. denticulate) continuously assimilated to cyanobacteria species in combination with zooplankton and detritus, probably due to detoxification capacity. Indeed, the aquatic plants (I. pseudoacorus) seem to be nutrient uptakes in water column and inhibit to light attenuation, comparing to cyanobacteria species. As a primary consumer of phytoplankton, zooplankton (Copepoda) consumed to small and edible particles which is changed from inedible toxic filamentous cyanobacteria species through the grazing efficiency by aquatic organisms. However, various kinds of fishes hardly feed on toxic cyanobacteria directly. Our result suggests that the native species, like Sinanodonta sp. and C. denticulate, are very useful bio-control organisms on toxic cyanobacteria bloom rather than carnivore, omnivore and planktivore fish. Furthermore, if an aquatic plant that can not only remove nutrients but also provide habitats to aquatic organisms (zooplankton, bivalves and shrimps) is developed, it can help control toxic cyanobacteria blooms. Therefore, it is considered that the development and establishment of habitat of useful organisms is very necessary for water quality improvement. Our biomanipulation technique may provide a key tool for efficient management and restoration of eutrophied reservoirs.