This work aimed to evaluate the effect of protein-based diets on phytoplankton composition and dynamics stocked with African catfish fingerlings Clarias gariepinus.Plankton samples were collected from 12 earthen ponds 400 m² which stocked with 40.07 ±1.12 gm fish (4000 fingerlings each). Poultry by-product meal was used to substitute fish meal as a source of the animal protein in a 25% protein pelleted feed for C. gariepinus. Experimental diets (25% protein), with fish meal protein replaced by protein from poultry by-product meal at three levels 0% (D₀), 35% (D₃₅) and 70% (D₇₀) were manufactured, fed to C. gariepinus fingerlings and the rearing period lasted for ~12 months. All treatments were characterized by both increasing in the chlorophyll “a" content and decrease in secchi disk readings with time.   The data showed that the algal composition represented by the four divisions Cyanophyta, Chlorophyta, Bacillariophyta and Dinoflagellates. The diet ponds fed on D₇₀ had significantly the highest standing crop of phytoplankton compared to all other treatments (p < 0.05). Most of this production consisted of blue green algae approximately 64-90 % of phytoplankton standing crop. Although the diet D₀ produced a high abundance of green algae but the diet with D₃₅ insignificant with D₇₀ in phytoplankton communities. The great abundance of blue-green algae caused the misuse of the diatoms, green algae and dinoflagellates which also accompanied by reduction in aquaculture yields. Although, the all treatments resulted in the flourish in the production of algal density but they did not lead to any significant increase in zooplankton abundance in all treatment. This is may be due to the fact that most of algal density in all treatments consisted of inedible blue-green algae which are unacceptable to zooplankton. Generally, it can conclude that there was insignificantly between D₀ and the D₃₅ in terms of algal community during in all seasons. So, we can replace the poultry by-product meal at level 35 % by fish meal for African catfish feed pellets.