The present study investigated the effects of lipid oxidation on quality deterioration in the ordinary and dark muscles of skipjack tuna Katuwonus pelamis during the early stages of ice storage for 72 h. The lipid hydroperoxide content of the dark muscle was significantly higher (P < 0.01) than that of the ordinary muscle throughout 72 h of ice storage. The metmyoglobin content of the ordinary muscle gradually increased, and was accompanied with darkening in the fish meat color. On the other hand, the addition of sodium ascorbate or 6-hydroxy-2,5,7,8-tetramethylchroman-2-carboxylic acid (Trolox®) to the ordinary muscle of skipjack tuna significantly inhibited the formation of lipid hydroperoxide as well as metmyoglobin formation. Thus, a decrease in α-tocopherol content in the ordinary muscle with antioxidant addition was not observed during ice storage period. In conclusion, the rate of lipid oxidation of skipjack tuna ordinary muscle is closely related to metmyoglobin formation, and the addition of antioxidants to fish meat is effective at inhibiting lipid oxidation as well as myoglobin oxidation in post-mortem meat.