Paralytic shellfish poisoning (PSP) toxins can be accumulated by bivalves through feeding process, therefore knowledge on the feeding and assimilation of PSP toxin containing algae are critical for understanding the kinetics of PSP toxins in these bivalves. In South China Sea, it has been documented that scallop Chlamys nobilis has much higher PSP toxin burden than the clam Ruditapes philippinarum. Experiments were therefore carried out to assess whether the difference of toxin burden between these two bivalves was due to the difference in feeding and assimilation. In the mixed diet of Alexandrium tamarense (a PSP toxin producing dinoflagellate) and Thalassiosira pseudonana (a non-toxic diatom), the two bivalves exhibited the same maximum filtration rate (equivalent to about 50% of the tissue dry weight per day) at 500 cells/ml of A. tamarense. At 100 cells/ml of A. tamarense, the maximum clearance rate of scallop (11 L/g/h) was significantly higher than the clam (7 L/g/h). Furthermore, the clams were able to produce pseudofeces at a lower cell density than the scallops. However, we found that the clams were unable to selectively exclude the toxic dinoflagellate by pseudofeces production. In scallops, both the assimilation efficiency (AE) and the gut passage time (GPT) were similar between A. tamarense and T. pseudonana. Clams however had a higher AE on T. pseudonana than on A. tamarense, but the GPTs were comparable for both algal diets. In general, AE decreased with increasing concentration of A. tamarense. Thus, it is likely that a higher PSP toxin level in scallops was due to: (a) a higher clearance rate; (b) no pseudofeces production at a relatively high algal density; and (c) slower detoxification, which is currently under investigation.