This study examined the right and left otoliths of 174 individuals of Pseudotolithus senegalensis from the Porto-Novo lagoon, Lake Nokoué and the Atlantic coast. The results show a significant variation in the population according to geographic location. Mixed-effects linear analysis showed no significant variation by site, side or sex (p > 0.05). Analysis of otolith shape using ANOVA showed significant differences for length, width and area (p < 0.05), but not for perimeter (p > 0.05). Canonical discriminant analysis revealed significant differences between sites (p < 0.05). Finally, shape analyses showed significant differences between sites (p = 0.0001) and between right and left sides (p = 0.007), but no difference by sex (p = 0.395). The study of otolith morphology is therefore proving to be a valuable tool for differentiating stocks and understanding ecological variations.