Intra- and interspecific chemical signals allow bacteria to respond to environmental conditions by regulating gene transcription. In cyanobacteria, gene products and the presence of fixed nitrogen regulate heterocyst frequency. In this paper, we describe a chemical made by a green alga, Chlamydomonas reinhardtii, that suppresses heterocyst formation in the co-occurring cyanobacterium, Anabaena flos-aquae. Cyanobacterial heterocyst frequencies were reduced in the presence of water-soluble, proteinase- and heat-resistant molecules greater than 15 kDa in molecular size. Green algal cells in all phases of growth made the suppressor. Ammonium and nitrate concentrations in the medium did not correlate with this change in phenotype. In addition, growth rate was not enhanced by the extracellular products. Therefore, C. reinhardtii extracellular products acted as a heterocyst inhibitor, not as a fixed nitrogen source. Chemical interactions between green algae and cyanobacteria influence heterocyst formation, an important consideration in understanding the outcome of competition between these organisms and the dynamics of phytoplankton communities.