Abstract: In order to make photosynthetic bacteria reached the maximum number of viable cells in the shortest possible time,,the culture inoculation and liquid volume of agents for the mixed culture of natto and photosynthetic bacteria were studied.with orthogonal test.The results showed that 20% of photosynthetic bacteria inoculation,natto inoculum 2%,agent liquid volume 60%in 250 mL flask culture was the best.The effects of mixture culture of photosynthetic bacteria and natto bacteria on the degradation of nitrite nitrogen and ammonia nitrogen in aquaculture water were also studied.The results showed that the best effect was received when two kinds of bacteria was mixed at 1∶1(v∶v),and the amount of mixed bacterial agents was positive correlation with the degradation of nitrite.Because natto bacteria could transfer organic nitrogen of medium into ammonia,so the increasing of the added amount of mixed inoculant weakened the degradation effects of ammonia nitrogen in aquaculture water.