Abstract The objective of this study was to describe the morphology and morphometry of saggitta otoliths of Polydactylus virginicus, Menticirrhus cuiaranensis and Conodon nobilis in a tropical environment. Fishes were caught with rod and reel in competitive fishing events promoted in 2014-2015 along the coast of Sergipe. A total of 174 pairs of sagitta otoliths of P. virginicus, 181 of M. cuiaranensis and 77 of C. nobilis was extracted. In general, the sagitta otoliths of all three species analyzed here presented different morphology and shape indices. The permutational multivariate analysis of variance (PERMANOVA) demonstrated significant differences among species and ontogenetic phases within each species using morphometry and shape indices. The linear discriminant analysis (LDA) presented a 98.3% correct reclassification of the otoliths by species.