Chub and blue mackerels are popular fish resources in Korea, but little is known about each biochemical characters of different anatomical regions. To investigate biochemical characters of chub and blue mackerels, three ordinary muscle regions were identified by their fin position; namely anterior, median, posterior. In addition, red muscle, as a dark muscle, was obtained from beneath the lateral line to compare with ordinary muscles. Proximate and lipid-class compositions did not show any discernible trends in the different anatomical ordinary muscles from mackerel of the same kind, while significant differences between ordinary and red muscles in the same mackerel, or between chub and blue mackerels, were observed. Red muscles from both mackerels had higher levels in lipids with higher neutral lipid class compared with ordinary muscles. The major difference between chub and blue mackerels was the levels of lipids and neural lipid class, indicating that all muscles from chub mackerel showed higher levels of neural lipids compared with those of blue mackerel (P<0.05). Fatty acid compositions showed that the percentage of polyunsaturated fatty acids (PUFA), especially docosahexaenoic acid (DHA, 22:6n-3), in median and posterior was higher compared with anterior muscle from both mackerels. When compared with chub mackerel, blue mackerel showed higher percentage of DHA in all muscle regions. In amino acid analysis, taurine concentration was much higher in the red muscle than in the ordinary muscles. But levels of histamine, glutamic acid, leucine and lysine were higher in the ordinary muscles. Our results indicated that chub mackerel contained more lipids than blue mackerel and that red muscle had higher levels of neural lipid and taurine compared to ordinary muscles.