Stable isotope tracers were first applied to evaluate the Microcystis cell assimilation efficiency of bivalves, since the past identification method has been limited to tracking the changes of each chl-a, clearity, and nutrient. The filter-feeders (Sinanodonta woodiana and Unio douglasiae) were assessed under the condition of cyanobacteria (Microcystis aeruginosa) blooms through an in mesocosm experiment using 13C and 15N dual isotope tracers. Chl-a concentration in the treatment mesocosm was dramatically decreased after the beginning of the second day, ranging from 116 to 66 μg L−1. In addition, the incorporated 13C and 15N atom % in the S. woodiana bivalve showed higher values than U. douglasiae bivalves. The results demonstrate that U. douglasiae has less capacity to assimilate toxic cyanobacteria derived from diet. Our results therefore also indicate that S. woodiana can eliminate the toxin more rapidly than U. douglasiae, having a larger detoxification capacity.