Saccular otoliths (sagittae) have long been shown to be species-specific and exhibit inland geospatial intra- and interpopulation morphological differences with variations in environmental conditions. Here, we analysed inland and outland geospatial variations in sagittae shape, length (Lo), width (Wo), perimeter (Po), and area (Ao), and fluctuating asymmetry (FA) in Chelon auratus males and females collected from Ghar El Melh (Tunisia) and Etoile Bay (Mauritania) stations to assess whether sagittae shape and morphometry differ between these two niches having different environmental conditions. At the intrapopulation level, a significant otolith shape asymmetry was observed between left and right and left–left and right–right otoliths among males and females of the Ghar El Melh (Tunisia) population and a significant symmetry among those of the Etoile Bay (Mauritania) population. At the interpopulation level, a significant asymmetry was found between left and right otoliths' shape among males and females of the two populations. Besides, a discriminant function analysis of otoliths' contour shape separated left and right otoliths among males and females at the intra- and interpopulation levels and also separated those of the two populations. Moreover, differential significant asymmetry in Lo, Wo, Po, and Ao between left and right otoliths was observed among males and females at the intra- and interpopulation levels. Therefore, the geospatial variations in environmental conditions between the two ecological niches effectively induced differences in otolith morphology. These significant asymmetries were discussed in terms of FA caused by environmental stress conditions resulting from variations in abiotic factors between the two ecological niches.