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The study investigated the bioactive molecules composition of microalgae biomass harvested from the fish culture system in the National Institute for Freshwater Fisheries Research, New Bussa. The isolated compounds were characterized using matrix-assisted laser desorption/ionization timeof flight mass spectrometry (MALDI-TOF-MS). The compounds characterized were amino acids. Cysteine (17 %) and Alanine (14 %) respectively were the predominant amino acids in the isolated compounds. The composition of essential, non-essential and semi essential amino acids were 20, 51, and 13 percent respectively. Results from this study will provide new knowledge about the bioactive ingredient composition of microalgae which shall be helpful to feed nutritionists in their search for feed materials that can substitute for fishmeal. Keywords: Amino acids, Microalgae species, Peptide chain, Nutritional