The following is a study of the trophic niche of Phrynops rufipes revealed by an investigation of stomach flushing and fecal samplings. We successfully stomach flushed all 31 adult turtles captured and collected feces from ten of the flushed turtles. Our results show that only an integrated approach using both techniques is able to provide a comprehensive picture of P. rufipes diet. Trichoptera larvae were the most eaten item in numeric terms and in frequency of occurrence, but shrimp contributed the greatest volume of invertebrates. The seeds of most kinds of palm trees common around streams in the area were eaten. Due to the limitations of stomach-flushing technique, palm fruits were underestimated, but they still contributed the highest volume of material flushed from the stomachs and found in the feces. Our findings alter the conclusions concerning the food habits of P. rufipes: it is an omnivore species that feeds in an opportunistic way on a greater quantity of benthonic macro-invertebrates and fishes than was evident from previous studies based on fecal sampling alone.