The Mn concentrations in the sagittae otoliths of 12 fish families (and 19 species) that co-occur in a coastal area of southeastern Brazil (~21°S) were quantified using electron paramagnetic resonance (EPR). Inferences were made about the relationship between fish habitat and trace element incorporation. Inferences were made on the relationship between trace element concentration and otolith shape. The differences in Mn concentrations among the species suggest that habitat (and feeding habits) might drive the incorporation of this trace element into fish otoliths, with higher values in bottom-associated fish species than in surface-associated species. In surface-associated fish species, the correlation between trace element concentrations and otolith shape was stronger than in bottom-associated species. Thus, while the Mn bioavailability in a fish's habitat, especially from feeding resources, is a local driving influence of trace element incorporation in sagittae otoliths, species-specific requirements also have an influence. Quantitative EPR is a non-destructive technique that is very useful when the available samples cannot be damaged, like with otolith collections.