The lipid and FA compositions of various organs and of the stomach contents of Scomber australasicus were analyzed. DHA was characteristically the major FA of all the major lipid classes of all organs except for liver TAG. The mean DHA contents of the various organs accounted for more than 17% of the total FA (TFA), whereas those in the stomach contents, originating from the prey, fluctuated and were generally low. In particular, the DHA levels in the TAG from all organs of S. australasicus accounted for up to 17% of TFA, even though it is a neutral depot lipid. S. australasicus contained markedly high levels of DHA, even though it is a small-sized Scombridae species, and its high levels of DHA were close to those in large-sized highly migratory tuna species. Furthermore, DHA levels in its muscle TAG were consistently high, compared with those in the visceral TAG, which might be directly influenced by the prey lipids. These phenomena suggest that long-distance migration has a close relationship with high accumulation of DHA in fish tissues, since S. australasicus is reported to migrate in offshore water, similar to highly migratory tuna species. Additionally, the physiological selective accumulation of DHA in the muscle during migration is caused by in vivo metabolism of FA in the vascular system, suggesting that DHA is poorly used as a source of migration energy, though it is provided abundantly through the prey lipids.