Among the growing serious problems concerning the quality of surface water is the occurrence of toxin-producing cyanobacteria. During their bloom, Microcystis aeruginosa produce microcystins, which has been found in epidemiological studies and animal laboratory tests to cause hepatic damage and promote tumor. With the ultimate goal of controlling the presence of cyanobacterial toxins in surface water, this study aimed to determine the toxin production behavior of toxic M. aeruginosa in the presence of a non-toxic Microcystis strain. Two cultures of similar growth media and initial N and P levels were prepared except that one was a pure culture of a toxic strain while the other is a mixed culture of toxic and non-toxic strains of M. aeruginosa of similar initial total cell concentrations. The cell density of the toxic strain, which was obtained using real-time PCR, nitrate, phosphate, pH, intracellular and extracellular toxin levels were monitored for 25 days. The toxic strain cell density in the mixed culture was found to be higher than that in the pure culture of the toxic strain. The rates of nitrate and P consumptions in the mixed culture were higher than that of the pure culture indicating that both toxic and non-toxic strain were consuming the nutrients. The extracellular and the intracellular toxin levels found in the culture where both toxic and non-toxic strains were present were higher than those of the pure toxic culture. The difference in toxin levels over the culturing period showed a maximum of 184.66µg/L for extracellular toxin and 457.77 µg/g-DW for intracellular toxin. Thus, it may be more dangerous if there are different strains of the same species of M. aeruginosa blooming together in a water body.