The diets of frugivorous animals result from the interaction between feeding preference and ecological factors such as availability of alternative resources and interactions with other frugivores. A better understanding of frugivore diets will enable predictions about the vulnerability of plant populations to anthropogenic or natural environmental changes. In addition, frugivores with greater variation in diet (generalists) are potentially more resilient to habitat changes than specialists. Here, we combined data on diets of frugivorous fishes with visual censuses on fruit availability to evaluate if fishes are selective or opportunistic in their use of fruits in floodplain habitats. We found a high diversity of fruit species (74 species) frequently consumed by four common species of frugivorous fishes during the flooding season. The identity of preferred fruits, rather than their availability, had a stronger effect on the patterns of fruit consumed by fishes in this system. Fruit preferences by fish may influence the long-term persistence and the maintenance of plant diversity in floodplain habitats. Possible disturbances of fish populations with selective consumption and the plant populations on which they depend could increase the vulnerability of both populations involved. Thus, selectivity may affect ecological and evolutionary processes associated with frugivory by fish.