Establishing predator–prey relationships and determining competitive interactions within the plankton community remains a central aim of zooplankton ecology. Using bivalve larvae as a model system, a DNA-based dietary approach using general eukaryotic primers was evaluated. Prey DNA was preferentially amplified using a predator-specific endonuclease restriction enzyme and blocking primer. Application of the blocking primer in isolation resulted in 80% of recombinant clones carrying inserts of non-bivalve origin, increasing to 100% when combined with a restriction enzyme. Further validation was achieved using wild, naturally feeding larvae of Mysella spp. and Ostrea edulis. Of the sequenced clones, 75% originated from centric and pennate diatoms (Bacillariophyta). A further 16% originated from fungi representing the phyla Ascomycota and Basidiomycota. The remaining sequences belonged to flowering plants (Magnoliophyta), single-celled green algae (Prasinophyceae), potential parasites (Ichthyosporea), dinoflagellates (Dinophyceae) and brown algae (Phaeophyceae). No qualitative difference in diet was observed among these two particular species, although the diversity of prey observed suggests that this DNA-based approach is suitable for studying the trophic interactions of marine bivalve larvae. Furthermore, based on sequence alignments, slight modifications to the blocking primer sequence could adapt this basic approach to a wide diversity of consumers within the plankton community.