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Microalgae, a kind of conventional bait for bivalves, can increase the cost of shellfish aquaculture. On this basis, Ruditapes philippinarum spat was selected to evaluate the feasibility of using photosynthetic bacteria (PSB) and marine yeasts as microalgae substitutes. The results showed that the addition of bacteria obviously affected the growth status of spat. Firstly, the survival rate of spat in 5%, 40%, 50% and 70% PSB substitution groups as well as 5% and 40% yeast substitution groups was not significantly different from that in microalgae group (p > 0.05), but that in other substitution groups was significantly lower than that in microalgae group (p < 0.05). Secondly, the growth rate of spat in PSB substitution groups (except for the 10% PSB substitution group) was significantly higher than that in microalgae group, and the 5% PSB substitution group had a growth rate which was 109.55% higher than that in microalgae group. There was no significant difference in the growth rate between microalgae group and 10%, 40%, 50% and 70% yeast substitution groups. Thirdly, the addition of bacteria also affected the digestive ability of shellfish. Pepsin enzyme activity in 20% PSB substitution group was 29.85% higher than that in microalgae group. Moreover, 5% and 40% yeast substitution groups had no significant difference in the pepsin enzyme activity compared with microalgae group. Finally, the nitrogen (N) and phosphorus (P) concentrations in the bacteria addition treatments were higher than those in the control treatment at the end of the experiment, but they were generally maintained at lower levels. In conclusion, it is feasible to partially replace microalgae with PSB and marine yeasts, and it is suggested that shellfish culture should be combined with wastewater utilization to promote the healthy development of aquaculture industry.