Alexandrium tamarense is a prominent harmful algal bloom forming species known to produce paralytic shellfish poisoning toxins (PSTs), as well as bioactive substances acting as allelochemicals. These specific allelochemical substances have not yet been structurally elucidated, but they have strong negative effects on a broad array of species, including many auto- and heterotrophic microplankton. The impact, however, of allelochemicals on actual bloom formation is currently under debate. Here we show the potential effect of allelochemicals on reducing grazing pressure on A. tamarense, while additionally demonstrating positive effects on the intra-population level. We established an allele-specific quantitative PCR (asqPCR) assay based on two A. tamarense microsatellite markers. The application of asqPCR distinguishes among three different strains of A. tamarense (A2, A4 and A5) in a mixed assemblage. Strain A2 expressed strong allelochemical activity, while A4 was only moderately lytic against targets and A5 was not lytic at all. All strains were grown individually, mixed either pairwise with each other, and/or pairwise together with a common protistan grazer, the dinoflagellate Polykrikos koifidii. When offered individual Alexandrium strains, the predator clearly grazed upon A5, moderate on A4 yet not upon A2. In pairwise mixtures, however, no prey strain-selection was observed. Finally, we show that the ecological concept of facilitation, invoking positive species interactions (here intra-specific), is a plausible explanation for the role of allelochemicals for natural populations of Alexandrium and their success in bloom formation.