Abstract Marine organisms have attracted considerable attention in recent years. In this study, peptides with osteogenic activity from Pinctada martensii were isolated and identified. Additionally, the effects of the hydrolysates on MC3T3-E1 cell proliferation and differentiation were evaluated using the MTT and alkaline phosphatase (ALP) assays, respectively. First, trypsin, pancreatin, and neutral protease were used to hydrolyse the intact shellfish. The hydrolysates with the greatest effects on osteoblast proliferation and ALP activity were separated and purified. Second, fraction WP2 was isolated and purified using a Sephadex G-25 column. WP2, which had the highest osteogenic activity, increased cell growth by 48.57 ± 0.05% and ALP activity by 6.27 ± 0.07 mU. Finally, four novel peptides were identified in WP2 (FDNEGKGKLPEEY, IVLDSGDGVTH, IVLDSGDGVSH, and SSENSDLQRQ) by Orbitrap Fusion Lumos Tribrid orbital liquid chromatography-mass spectrometry. Our findings revealed that P. martensii contains peptides with potential osteogenic activity.