Fluctuating asymmetry (FA) is assumed to reflect the developmental instability caused by environmental or genetic stress. Fish otoliths represent a very good tool for investigating the consequence of different effects on FA. Otolith FA analysis, coupled with genetic analysis, has been undertaken on two common West African estuarine species, Ethmalosa fimbriata (EFI) and Sarotherodon melanotheron (SME), in two neighbouring estuaries, in order to highlight the impact of salinity on developmental stability. The Gambia estuary has a normal functioning and the Saloum estuary is inverse (saltier waters in the upper river), reaching extremely high salinities (>100 psu) and constituting severe environmental stress. Five sub-populations of EFI and six of SME were studied along a salinity gradient. The differences between right and left otoliths were estimated with image processing by measuring five dimensions (area, perimeter, diameter, rostrum and posterior radii). Analyses of genetic differentiation at three EPIC and one anonymous nuclear gene loci for EFI and six polymorphic enzymatic loci for SME were carried out to measure the level of heterozygosity. Absolute FA in all otolith traits examined was unaffected by gender but increased significantly with fish size. Size-corrected absolute FA did not show any significant difference among sites differing largely in salinity, although a higher asymmetry in otolith area was recorded in the saltiest site. These findings suggest that otolith asymmetry is a poor indicator of osmotic stress. The individual heterozygosity level did not seem to have an effect on otolith FA for either species, even though a slight correlation appeared with otolith area or perimeter. Otolith FA cannot be considered to be a useful indicator for estimating changes linked with environmental or genetic stress in these estuaries.