In a tropical reservoir, the cyanobacteria Microcystis aeruginosa and Cylindrospermopsis raciborskii are the dominant species, with changes in dominance throughout the year. Since allelopathy has been suggested as a factor that could promote or stabilize harmful algal blooms, we investigated potential allelopathic effects of C. raciborskii on M. aeruginosa. Microcystis aeruginosa was exposed to exudates of a C. raciborskii monoculture and exudates of mixed cultures of both species. Significant growth inhibition of M. aeruginosa was observed only when it was exposed to exudates from the mixed culture with high proportion of C. raciborskii. This result suggests that the production of growth inhibitors seems to depend on stress (competition) and on the density of the producer species. In contrast to the control, M. aeruginosa formed colonies when exposed to filtrates of mixed cultures. As far as we know, this is the first report on colony induction resulting from the interaction between cyanobacteria. Our results suggest that compounds produced by C. raciborskii may induce defense mechanisms in M. aeruginosa. Our results also indicate specificity in this interaction, since another strain of M. aeruginosa showed different responses.