Otolith shape is species-specific in fish. In this study, 161 samples of Trumpeter sillago Sillago maculata and 164 of Silver sillago Sillago sihama were collected from Beibu Gulf in July 2009. The main objective of this study was to use morphological variables and Fourier harmonics to describe otolith characteristics and use discriminant analyses to separate the two species. Otoliths were measured by traditional one and two dimensional measures(otolith length, width, diameters, area, perimeter, rectangularity and circularity), as well as by Fourier analysis to capture the finer regions of the otolith. Analysis of covariance(ANCOVA)showed that there was significant correlation between morphological variables(diameter, perimeter, otolith length, otolith width, otolith area, density, harmonics 3, harmonics 4, harmonics 5, harmonics 13, harmonics 15, and harmonics 16)and body length. To minimize size effects on the morphological variables between species, only fish with a body length between 90 and 140 mm were included in the data analysis and the variables which had significant relation with body length were transformed using the residual. The result showed that the accuracy of discriminant analysis was 97. 8% and 100% for Trumpeter sillago and Silver sillago, respectively. This high accuracy indicated that otolith shape was described accurately by morphological variables and Fourier harmonics, and discriminant analysis was an effective way to identify and separate the two species.