Centropomus undecimalis and Centropomus ensifurus are a species belonging to the family Centropomidae, which has an important role in estuarine ecosystem. The present study aimed at comparing the otoliths shape of juveniles both species collected in in the lower São Francisco River (10°28′34.02″S, 36°24′27.02″W). In the laboratory, 52 otoliths were extracted, photographed, measured and the contour was analyzed by the wavelet method. The otolith contours varied between species (n = 28 C. ensiferus and n = 24 C. undecimalis). The Linear Discriminant Analysis correctly reclassified 92.3% of all otoliths among species. MANOVA also evidenced significant differences in contour between species (F = 3.73; p < 0.0001). The results suggest that C. ensiferus is adapted to enviroments with higher turbidity and the C. undecimalis tends to colonize environments with lower turbidity and spends more time in the water column.