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Disruption methods used to extract proteins from the cell often require optimization in terms of yield increase and molecular integrity according to the cell type. Most cell lysis methods primarily target the cell wall. However, even for the wall-deficient strains, efficient extraction of molecules in or attached to membranous structures is a delicate process. In this study, we optimized the protein extraction technique for a cell wall deficient strain of Chlamydomonas reinhardtii, which is also a preferred material for most of the recombinant protein production studies. Liquid nitrogen (LN) was evaluated for efficient protein extraction from wall-less strain. The results were compared with sonic treatments, which were optimized in terms of applied power and duration. The results showed that sonication at 25% power for 20 seconds of three rounds provided optimum results for the protein integrity and extraction yield (74.13±2 µg/mL and 185.32±5 mg/g). Although LN has provided similar results in terms of protein content compared to sonication, (70.15±4.43 µg/mL and 175.37±11.09 mg/g maximum), it revealed low efficiency in extracting intact proteins from sub-compartments of the cell.