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. 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 and their application 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. 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, no prey strain-selection was observed. 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.