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Otoliths are known to vary in morphology between and within species and therefore, they have long been considered useful structures for fish identification and discrimination in numerous studies. To obtain a deeper understanding of whether the shape of the sagitta otolith shows a discrepancy between congeneric species and their sexes inhabiting the same environmental conditions, it was found useful to compare the shape of the sagitta otolith between fish samples and the sexes of Liza aurataand Chelon ramadacollected from the Boughrara lagoon situated in southeastern Tunisia using Elliptical Fourier analysis (EFA). At the interspecific level, the MANOVA and Wilks’ λ tests showed significant differences (p< 0.0001), i.e., asymmetry, between the left and right otoliths of the two species. At the intraspecific and intersexual levels, the Fisher’s distances (D) showed significant asymmetry in the otoliths (p < 0.05) between males and females on the left and right sides, as well as between the right sides, i.e. there was sexual dimorphism. Besides, a significant asymmetry between the left and right sides of the otoliths was found between males, as well as between females in L. aurata. However, in C. ramada, significant asymmetry was detected only on the right and left sides of the otoliths between males and females, i.e. there was sexual dimorphism. Moreover, the modality projection on the first two axes F1and F2of the Redundancy analysis (RDA) accounted for 60.11% of the total variance and clearly showed the presence of two distinct main groups of otoliths corresponding to the two species. Therefore, the shape of the saccular otoliths, sagittae, showed clear variation, i.e. asymmetry, between L. aurataand C. ramada, as well as between the sexes. This variability in the sagitta otolith shape was suggested to be due to differences in the response and adaptability of the fish samples of both species to the local environmental conditions of the Boughrara lagoon.