Sea urchin gonads have been demonstrated to contain major yolk protein (MYP), which can be hydrolyzed by enzymes to release biologically active peptides. The in silico analysis of the MYP sequence in the BIOPEP database showed the presence of fragments with antioxidant activity. The sequence was hydrolyzed by 21 kinds of proteases and 23 antioxidant peptides were obtained. Eight peptides, including Leu-Trp (LW), Arg-Trp (RW), Ala-Trp (AW), Thr-Trp (TW), Ala-Asp-Phe (ADF), Leu-Trp-Lys (LWK), Ser-Asp-Phe (SDF) and Leu-Tyr (LY), were screened and a score over 0.5 was obtained using PeptideRanker. The peptides LW, TW and LWK showed a stronger antioxidant capacity with IC50 values of 8.85, 9.59 and 9.62 mmol L-1, respectively, compared to that of glutathione (10.81 mmol L-1). Furthermore, AW, LW and LY showed Trolox equivalent antioxidant capacity (TEAC) values of 3.07, 1.87 and 1.52 mmol TE per mmol peptide, respectively. These results suggest that the MYP from sea urchin (S. nudus) gonads is a good source of antioxidant peptides with abundant tryptophan.