Populations of the toxigenic marine dinoflagellate Alexandrium are composed of multiple genotypes that display phenotypic variation for traits known to influence top-down processes, such as the ability to lyse co-occurring competitors and prospective grazers. We performed a detailed molecular analysis of species interactions to determine how different genotypes perceive and respond to other species. In a controlled laboratory culture study, we exposed two A. fundyense strains that differ in their capacity to produce lytic compounds to the dinoflagellate grazer Polykrikos kofoidii, and analyzed transcriptomic changes during this interaction. Approximately 5% of all analyzed genes were differentially expressed between the two Alexandrium strains under control conditions (without grazer presence) with fold-change differences that were proportionally higher than those observed in grazer treatments. Species interactions led to the genotype-specific expression of genes involved in endocytotic processes, cell cycle control and outer membrane properties, and signal transduction and gene expression regulatory processes followed similar patterns for both genotypes. The genotype-specific trait changes observed in this study exemplify the complex responses to chemically mediated species interactions within the plankton and their regulation at the gene level.