Toxic attributes of the brown tide alga Aureococcus anophagefferens affect the ability of benthic and protistan grazers to control blooms. Yet, little is known regarding the effect of A. anophagefferens on a dominant component of the microzooplankton community, copepod nauplii. This study describes the grazer–prey relationship between nauplii of the calanoid copepod Acartia tonsa and A. anophagefferens. Four laboratory experiments using varying proportions of A. anophagefferens (2–4 μm) and a control alga, Isochrysis galbana (4–6 μm), were conducted to test the effects of A. anophagefferens isolate 1708 during exponential and stationary growth phases and A. anophagefferens isolate 1850 (exponential phase only) on naupliar grazing and development. A fifth experiment compared the effects of A. anophagefferens with an equal-sized control alga, Micromonas pusilla (1–3 μm). Isolate 1708 (exponential or stationary) as a single food item did not suppress naupliar ingestion rates (ng C nauplius−1 day−1) when compared to I. galbana. No ingestion was detected on isolate 1850 when offered alone, suggesting that this isolate may be more harmful to nauplii. Overall, nauplii selectively grazed on I. galbana over A. anophagefferens in mixed diets, but size-selection could not be ruled out as selective feeding was not apparent in mixtures with M. pusilla. Both isolates of A. anophagefferens delayed naupliar development. Our results indicate that Acartia tonsa nauplii can graze on A. anophagefferens, and can potentially help suppress brown tides. However, the efficacy of grazing control by copepods will vary with availability of alternate food sources and toxicity of the A. anophagefferens strain(s) comprising the population.