Abstract: Parasitic attack commercially important fishes are a matter of great concern. Parasites were collected from the Nagapattinam coastal environment, Southeast coast of India. The concentration of protein in the muscles shows variation among the isopods parasites. The muscle proteins from 5 species of isopods parasites was studied, among the species maximum protein content of 18.26% was observed in Nerocila loveni and the minimum protein content of 3.44% was noticed in Catoessa boscii. After the Sodium Dodecyl Sulphate-Polyacrylamide Gel Electrophoresis (SDS-PAGE), their clear bands were detected in the gel that represents proteins from five species of isopods. The present study reported for the first time that muscles proteins of isopods were isolated and considered for protein quantification and identification.