Molecular approach for analysis of in situ feeding by the dinoflagellate Noctiluca scintillans

•The red tide forming species noctiluca scintillans is a marine heterotrophic dinoflagellate.•We analyzed the prey organisms within natural cells of N. scintillans using two genetic methods.•Restriction enzyme digestion and blocking primer methods were applied.•DNA sequences of surprisingly diverse taxa were obtained from the natural cells of N. scintillans.•Molecular prey analyses may reveal undiscovered interactions within the plankton community.