Geographic variability in sagittal otoliths shape of the Japanese Spanish mackerel (Scomberomorus niphonius) was studied to test whether stock discrimination might be possible using this method. It was hypothesized that S. niphonius would show little difference in otolith shape, likely as a result of mixing between seas. A total of 164 sagittal otoliths were collected from commercial fishing vessels between April and June 2010 in three spawning grounds, that of Qingdao in the middle Yellow Sea, Lvsi in the southern Yellow Sea, Huanghua in the the Bohai Sea. To minimize the potential effect of the fish size among the three fishing grounds, a narrow size range (400–550 mm fork length) was selected. The discriminant function analysis conducted with standardized otolith shape indices and Fourier harmonics produced classification success rates ranging from 57.0 to 88.2% and worked well in the separation between the Bohai Sea group and the Yellow Sea group. No significant differences were detected among the three groups for the Lvsi spawning grounds. The otolith variables showed a distinct gradual variation tendency with the movement of fish schools from south to north. The results suggest that stock from the Bohai Sea could be managed as a separate entity from those found in the Yellow Sea.