The study was conducted in order to compare the abundance, diversity, evenness and composition of phytoplankton in tilapia ponds fertilized with chicken manure and CLSU organic fertilizer. Three taxonomic groups of phytoplankton were observed in the four months sampling namely Chlorophyta, Cyanophyta and Chrysophyta. Abundance of Phylum Chlorophyta was higher in ponds fertilized with chicken manure. Mean diversity of the identified phytoplankton taxa in both types of fertilizer were very low across months of sampling. Even distribution of species was recorded in Phylum Cyanophyta and Phylum Chrysophyta using the two fertilizers. The uneven distribution of phytoplankton in Phylum Chlorophyta was due to very high composition of Oedogonium spp. The use of CLSU organic fertilizer led to higher composition of Chlorella spp. and Hydrodictyon spp. and these were recognized to have economic importance in aquaculture as food source.