Zooplankton grazing is often a significant loss term for phytoplankton populations, including harmful algae, impacting the development and decline of blooms. However, detecting and quantifying predation on phytoplankton is often challenging, particularly during early bloom stages when phytoplankton cell concentrations are low. In this study, we used polymerase chain reaction (PCR) to detect ingestion of toxic dinoflagellates of the Alexandrium tamarense species complex by two copepods, Acartia hudsonica (laboratory population) and Calanus finmarchicus (field population). Recent ingestion of Alexandrium fundyense cells was indicated by positive amplification of an LSU rDNA fragment specific to A. fundyense from whole copepod extracts. In laboratory experiments, A. fundyense DNA was detectable for 24 h post-ingestion in A. hudsonica fed A. fundyense, but not detected in animals fed other phytoplankton, or starved. In field samples, ingestion of A. fundyense by C. finmarchicus was confirmed by PCR, including at four stations where the A. fundyense concentration was ?14 cells L?1. At these low prey concentrations, ingestion rates on A. fundyense may have been as low as 1 cell copepod?1 day?1. Nevertheless, simulations of A. fundyense population growth suggest that a few predators L?1 have the potential to curb the early development of a slow-growing bloom, even if ingestion rates are extremely low. Low predation rates can still have a large impact when prey populations are small.