Although microcystins (MCs) are the most commonly studied cyanotoxins, their significance to the producing organisms remains unclear. MCs are known as endotoxins, but they can be found in the surrounding environment due to cell lysis, designated as extracellular MCs. In the present study, the interactions between MC producing and the non-producing strains of
Microcystis aeruginosa
, PCC 7806 and PCC 7005, respectively, and a green alga,
Desmodesmus subspicatus
, were studied to better understand the probable ecological importance of MCs at the collapse phase of cyanobacterial blooms. We applied a dialysis co-cultivation system where
M. aeruginosa
was grown inside dialysis tubing for one month. Then,
D. subspicatus
was added to the culture system on the outside of the membrane. Consequently, the growth of
D. subspicatus
and MC contents were measured over a 14-day co-exposure period. The results showed that
Microcystis
negatively affected the green alga as the growth of
D. subspicatus
was significantly inhibited in co-cultivation with both the MC-producing and -deficient strains. However, the inhibitory effect of the MC-producing strain was greater and observed earlier compared to the MC-deficient strain. Thus, MCs might be considered as an assistant factor that, in combination with other secondary metabolites of
Microcystis
, reinforce the ability to outcompete co-existing species.