Variations in sagittal otolith shape and morphometry, including length (Lo), width (Wo), area (Ao), and perimeter (Po), were investigated in two populations of Chelon ramada collected from the Boughrara and El Bibane lagoons located in southeastern Tunisia. The objective was to assess the geographic variation in the sagittal otoliths' shape and morphometry and the effect of potential fluctuating asymmetry (FA) in morphometry on the stock structure of C. ramada in the two lagoons to inform on appropriate management procedures. At the interpopulation level, analysis of sagittal otolith shape showed a statistically significant difference (P = 0.0001), i.e. there was a bilateral asymmetry, in the shape of left and right otoliths between individuals of the two populations. In addition, significant FA was found only in Lo between the left and right otoliths. At the intrapopulation level, a significant shape difference (P < 0.0001), particularly asymmetry, was observed in both left and right otoliths between males and females, indicating sexual dimorphism in shape within the Boughrara lagoon. However, significant shape similarity, i.e. symmetry, was observed in the left and right otoliths among individuals of the El Bibane lagoon. Moreover, a significant FA was detected in Lo between the left and right otoliths only among males, as well as between males and females of the Boughrara lagoon. However, a significant FA between the left and right otoliths was found only in Wo among males and in all morphometric dimensions among females and Wo between males and females of the El Bibane lagoon. Discriminant function analysis of the otolith contour shape confirmed the presence of two separate C. ramada stocks, one corresponding to the Boughrara lagoon and the other representing the El Bibane lagoon, which should be managed separately. The possible cause of morphological variation in the sagittal otoliths' shape and morphometry due to FA between individuals of the two populations was discussed in relation to the biotic and abiotic factors.