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In this study, the whole proteins from a Chinese three-striped box turtle ( Cuora trifasciata) were extracted and hydrolyzed using three proteases (alcalase, papain, and protamex). By orthogonal experiments, the optimal hydrolysis conditions for producing peptides with the highest cancer cells growth inhibition activity were determined. Such as, the maximum inhibition on MCF-7 cancer cells (92.37% at 1 mg/mL) was achieved by papain hydrolysis (pH 8, 37 °C, enzyme-to-substrate ratio (E/S) 1.5%), and the maximum inhibition on HepG2 cancer cells (94.16% at 1 mg/mL) was reached by protamex hydrolysis (pH 8, 40 °C, E/S 2%). Using ultrafiltration and Sephadex G-15 column chromatography, two polypeptides M2 and F4 were isolated. At 500 μg/mL, M2 exhibited 74.7% and 62.9% of antiproliferation activities on MCF-7 and HepG2 cancer cells, respectively; and F4 displayed good inhibitory effects on MCF-7 (70.59%) and HepG2 (78.6%) cancer cells. M2 and F4 had lower inhibition (<20%) than drug 5-FU (>60%) on normal liver cells L-O2. Moreover, three peptides, EMLQPPL, PGKPLFL, and SCCSCDED, were identified; their inhibitory effects on cancer cells were confirmed after synthesis. These data, for the first time, demonstrated that Cuora trifasciata-derived proteins could be used for preparing antiproliferation peptides. [ABSTRACT FROM AUTHOR]