This study explores the interplay between digestive tract traits, food intake, and assimilation in omnivorous tetra fishes (Psalidodon bifasciatus, P. aff. gymnodontus, and Bryconamericus ikaa) from the Iguaçu River basin, an ecologically significant region known for high endemism. We hypothesize that variations in digestive tracts across species would be associated with differences in diet, isotopic composition in fish tissues, and overall diet assimilation. To test this, we employed stereoscopic and light microscopy to characterize the gross anatomy, histomorphology, and histochemistry of fish digestive tracts. Additionally, we used stomach content and stable isotope analyses to trace fish diets. While these tetra fishes shared histological structures, disparities were noted in anatomical digestive traits and diet preferences. The smallest species, B. ikaa, with a shorter intestine, had fewer pyloric caeca and primarily consumed animal‐based diets. Conversely, P. bifasciatus and P. aff. gymnodontus, with longer intestines, displayed numerous pyloric caeca and consumed a balanced mix of animal and plant items. Despite anatomical and dietary differences, all three species predominantly assimilated animal‐origin food. The tetra fishes had histological variations among digestive tract segments, with the esophagus having the thickest muscular layer, gradually thinning towards the posterior intestine. The final portion of the intestine exhibited a significant expansion in the lumen perimeter, while the esophagus had the smallest lumen area. Goblet cells were most concentrated in the posterior intestine for all species. The gross anatomy of these tetra fishes aligns with their omnivorous habit, while diet assimilation was dominated by animal‐origin food. These findings provide crucial insights into the structural and tissue characteristics of their digestive systems, laying the groundwork for deeper exploration into the physiological aspects of their digestive tracts and enhancing our understanding of their feeding strategies.