The morphology and morphometry of otoliths have emerged as powerful indicators of ecological characteristics of fishes. However, shape descriptors that can accurately predict well-documented functions played by species in tropical ecosystems are either restricted to a few groups or poorly known. Therefore, we evaluated the power of two otolith shape descriptors (ecomorphological indexes and Fourier harmonics) in discriminating trophic and depth strata preference groups of tropical fish species. Differences in otolith shape of ecological groups were visualized by linear discriminant analysis (LDA), and tested by a jack-knife cross-validation method and permutational multivariate analysis of variance (PERMANOVA) for both methods. Visually and statistically, both descriptors were good predictors of trophic groups and depth preference categories (PERMANOVA, p < 0.05). Overall jack-knifed classification success between both descriptors were very similar, with harmonics correctly classifying 90.38% of assigned trophic groups and 75.96% of given depth preference categories, against 82% and 56.25% of ecological indexes, respectively. Our results suggest that Fourier descriptors and ecomorphological indexes of otoliths should be used as functional traits in future studies, as otolith shape provides a wider range of ecological information regarding feeding habitat, mobility, substrate association and water column use.