The aim of this study was to test the effective separation of shape indices of otoliths of three species belonging to the family Sciaenidae before and after in vitro digestion. We measured 328 sagittal otoliths and applied six shape indices. Before the experiment, the aspect ratio (otolith height/otolith length%), circularity, ellipticity and relative surface of the sulcus acusticus were suitable for differentiating the species of genera Paralonchurus and Stellifer. Among the species of Stellifer, the aspect ratio and rectangularity were suitable. Otoliths exposed to in vitro digestion showed no significant differences in their morphometry before and after the experiment. After in vitro digestion, the aspect ratio and circularity were effective in separating Paralonchurus and Stellifer. However, none of the indices used in the present study were efficient to separate otoliths of congeneric species after in vitro digestion.