Resource partitioning has an essential role in interspecific relations, especially in congener species, which share many morphological traits. In some places, small characids coexist through resource partitioning, which may reduce their interspecific competition. Astyanax species (e.g., Astyanax minor, Astyanax gymnodontus and Astyanax bifasciatus), for example, coexist in different water bodies from the Iguaçu River basin. These species have high phenotypic plasticity and many morphologic specializations that allow them to live in different habitats. Based on evidences that these species modified their feeding habits because of changes in resource availability in Iguaçu River, this study tested two hypotheses: (a) there are differences in head morphology, number of teeth and number of gill rakers among the species of Astyanax; and (b) there are differences in gill arch and gill raker morphology among the species of Astyanax, which may favour their trophic resource partitioning in Iguaçu River. The head morphological traits and quantitative morphological characters were summarized in a principal coordinates analysis (PCoA), and the analysis of similarities (ANOSIM) showed significant differences among species. Gill morphological measurements were analysed through analysis of covariance (ANCOVA), and it also showed significant differences in gill arch and gill raker morphology among species. Therefore, the analysis of ecomorphological traits related to trophic habits revealed some differences that may suggest a tendency of reducing competition for trophic resources in the Iguaçu River basin.