Seasonal variation in fatty acid profiles was examined in the visceral mass and the posterior adductor muscle of the female pen shell, Atrina pectinata. Total percentages of saturated fatty acids were similar between the two organs, and there was not a prominent seasonal change in both tissues. While the percentages of highly unsaturated fatty acids (HUFAs) in the visceral mass were higher than those in the posterior adductor muscle, monounsaturated fatty acids (MUFAs) were high in the posterior adductor muscle. HUFA contents, especially in $20: 5omega3$, $22: 5omega3$ and $22: 6omega3$, markedly decreased in September in the visceral mass, and this decrease was associated with a corresponding total MUFAs in the same organ. A similar pattern of change in September was noted in the posterior adductor muscle MUFAs and HUFAs. These results indicate that $20:omega3$ and $22:omega3$ HUFA changes in the visceral mass and posterior adductor muscle reflect the reproductive stages in pen shell.