Abstract: Objective: To isolate and screen the bioactive oligopeptides which can promote bone formation from square siphon worm. Methods: Oligopeptides were prepared by enzymatic hydrolysis and membrane separation, and peptide sequences were identified by HPLC-MS/MS. The online database was used to predict drug formation, and the zebrafish model was used to evaluate the effect of promoting bone formation. Results: A total of 10 low molecular weight peptides were given. Two potential candidate peptides were obtained by zebrafish bone development models. Their amino acid sequences were GFAGDDAPR and GLGGLSPEK, which named GSP1 and GSP2. Molecular weights of two potential candidate peptides were 905.04 and 857.06 Da. Two potential candidate peptides could significantly promote the osteogenesis of juvenile zebrafish. Compared with the blank group, when Juvenile of AB zebrafish were treated with GSP1 solution (1~50 μg/mL), the area of integral optical density and green fluorescence increased in the skull of juvenile fish. When the concentration of GSP1 was 5 μg/mL, it had the best effect of promoting bone development. Compared with the blank group, when the juvenile of AB zebrafish were treated with GSP2 solution (1~50 μg/mL) , the area of integral optical density and green fluorescence increased in the skull of juvenile fish. When the concentration of GSP2 was 50 μg/mL, it had the best effect of promoting bone development. Conclusion: The oligopeptides less than 1000 Da were expected to be candidate drugs for promoting bone formation.