Based on the 46 samples of Sardinella aurita and 53 samples of Sardina pilchardus taken from the Chinese trawling vessel working in the Morocco coastal waters from June to August in 2011, their otolith morphology was analyzed based on traditional measurement and Fourier analysis. Six of variables were measured on the otolith and differences were compared by t-test; digitalized photographs of otolith were transformed to Ellipse Fourier descriptors (EFDs). Finally, six variables and 77 standardized EFDs were analyzed by principal component analysis (PCA) and stepwise discriminant analysis (SDA). The results showed that the total length (TL), total width (TW), dorsal width (DW), and ventral length (VL) had significant differences between two species (P<0.01), whereas dorsal length (DL) and wing length (WL) had no difference (P>0.05). Result of PCA showed that the first and second components made total contribution of mutation for 77.0% by traditional measurement, and the highest variables were total length/fork length (TL/FL) and dorsal width/fork length (DW/FL) respectively, the scatter-plot reveal a good dispersion; there were 16 principal components with 82.8% cumulative contribution by Fourier analysis, but the first two components had too much overlap with a bad separation. SDA showed that three variables of traditional measurement entered in the SDA, total correct classification was 83.76%; 9 harmonics of 77 EFDs entered in SDA with Fourier analysis, and the total correct classification was 92.02%. Overall, Fourier analysis is more effective than traditional measurement in the fish otolith morphology classification.