Diel changes in bacterial ingestion by a mixotrophic flagellate, Cryptomonas sp., and heterotrophic nanoflagellates (HNF) were examined in situ at 4-h intervals for 2 d in the epilimnion and metalimnion of Lake Biwa using bacteria-sized fluorescent microspheres as a tracer food. Clearance rates of HNF for the microspheres ranged between 1.3 and 4.5 nl cell-1 h-1, but the average rate did not differ between day and night. In contrast, clear diel changes were observed in the clearance rate of Cryptomonas sp. in the epilimnion from <0.5 nl cell-1 h-1 at midnight to >3 nl cell-1 h-1 at noon. In the metalimnion where light intensity was lower, however, the clearance rate of Cryptomonas sp. was always <0.5 nl cell-1 h-1 through the study period. Thus, bacterial ingestion of Cryptomonas sp. is not to acquire supplementary energy or carbon at low phototrophic activities. During the study period, both inorganic phosphorus and nitrogen concentrations were less than or close to the detection limits (10 nM P and 1 μM N) in the epilimnion, but much higher in the metalimnion. The results strongly support the idea that Cryptomonas sp. utilizes N and P from bacteria as substitutable nutrients when photosynthesis takes place under conditions of nutrient depletion. To assess the grazing effect of mixotrophic algae on bacterial populations, it is essential to consider diel changes in their phagotrophic mode of nutrition that are induced by light regime and nutrient concentrations in ambient water.