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The aim of this study, in the first step, was to recover the protein content in wastewater of fish meal factories using chitosan, chitosan nanoparticles and chitosan-aluminum sulphate composition. In the second step, the extracted protein was assessed for its  essential amino acids profile.  Also, the  reduced amount of proteins in the waste water was evaluated by measuring different parameters such as turbidity, pH, COD. Finally, chitosan nanoparticles characteristics were investigated using atomic force microscopy. Results showed that turbidity, COD and soluble protein significantly decreased upon  adding different concentrations of chitosan, nanoparticle of chitosan and chitosan-alum (p<0.05). The maximum protein recovery was related to chitosan-alum composition and chitosan nanoparticles with no significant difference between these two treatments. Evaluation of recovered protein in term of amino acids profiles showed that there were essential amino acids such as histidine, lysine, methionine and phenylalanine in protein of fish meal wastewater.