Harmful algal blooms (HABs) caused by the pelagophyte Aureococcus anophagefferens have spread globally and are a threat to coastal ecosystems. Although some HAB mitigation techniques such as algal biocides can be effective, many such approaches can have negative consequences on the environment. Therefore, it is important to investigate alternative HAB mitigation approaches that are ecologically safe and commercially viable. Here, we examine the effects of two rhodophyte seaweeds, Gracilaria tikvahiae and Dasysiphonia japonica, on A. anophagefferens. During experiments, multiple A. anophagefferens strains were co-cultured with densities of seaweed encompassing a range of environmental and aquaculture settings (0.25–3.00 g L−1). The co-effects of nutrients, heterotrophic bacteria and pH were also assessed, and A. anophagefferens cell concentrations and photosynthetic efficiency were quantified. In nearly all experiments, G. tikvahiae and D. japonica significantly reduced A. anophagefferens cell concentrations in a dose-dependent manner, with the effectiveness of each seaweed depending primarily on both A. anophagefferens and seaweed densities. The algicidal effects of D. japonica were significantly stronger than G. tikvahiae and other algicidal seaweeds (e.g., Ulva spp.). Allelopathy was the most potent mechanism for inhibition of A. anophagefferens; heterotrophic bacteria, nutrient limitation and elevated pH appeared to have lesser co-effects. These findings, in conjunction with the well-known nutrient removal capacity of seaweeds, suggest that the temporal and spatial dynamics of these rhodophytes may influence brown tides in shallow estuaries and that the use of seaweeds such as G. tikvahiae in aquaculture may be a promising mitigation strategy for this and other HABs in coastal ecosystems.