This study represents significant monthly variations of total lipid and fatty acid composition of muscle and liver tissue of Black Sea bonito (P < 0.05). Average total lipids of bonito muscle and liver were 8.4% and 25.1%, respectively, and the highest polyunsaturated fatty acid (PUFA) was observed in September and March as 52.9% and 46.6%, respectively. Bonito muscle was found to contain good amounts of eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) in a range of 252.0–1169.1 mg/100 g and 712.1–3324.1 g/100 g, respectively. Higher levels were found in liver at 3323.3 mg/100 g for EPA and 6996.5 mg/100 g for DHA. Although 25–100 g edible muscle is necessary to reach 1 g per day of EPA+DHA requirement for a healthy diet, only 9.8–87.9 g of bonito liver is enough to cover the recommended daily amount for these fatty acids. The results indicate that bonito livers constitute a rich and underexploited source of PUFAs.