This study was carried out to investigate the optimun conditions for the isolation of low molecular weight peptides containing histidine, and to evaluate the antioxidant effects of skipjack boiled extracts(SBE). The results are summarized as follows : L-histidine contents of the ordinary muscle and dark muscle extracts were $ 83.1{pm}1.75{mu}M/g;and;11.0{pm}2.39;{mu}M/g$, respectively. The L-histidine level of the dark muscle was much lower than that of ordinary muscle in the SBE. The extracts were treated with alcalase and neutrase under different pH levels, temperatures, and times. The optimum hydrolysis conditions of SBE were pH 7.0 and a $60^{circ}$C temperature for 2 hr in the batch reactor, which hydrolyzed 63% of the SBE. HPLC analysis showed a removing effect of the ultrafiltration permeate (UFP) to high molecular weight impurities in SBE. SBE and pure carnosine participated as inhibiting agents to, which was confirmed through the autoxidation processing of linoleic acid. UFP treatment improved the inhibiting ability of SBE to the autoxidation of linoleic acid. The reducing power of the UFP-treated ordinary muscle extracts were 10-fold higher than the dark muscle extracts, and 0.7-fold higher than 20 mM pure carnosine. The UFP-treated ordinary muscle extracts had greater reducing power activity than pure carnosine. The scavenging activities on DPPH radical of the different treated-SBE and pure carnosine were also investigated. Scavenging activities of the ordinary and dark muscle extracts and the pure carnosine were 90%, 70%, and 45%, respectively. In summary, Skipjack boiled extracts (SBE) demonstrated that low molecular weight peptides containing histidine are capable of inhibiting lipid oxidation. They also possessed effective abilities as free radical scavengers and reducing agents, and these activities may increase with increasing concentrations.