The influence of temperature and nutrients on the co-occurrence of Cylindrospermopsis raciborskii and Microcystis panniformis in Mundaú reservoir was investigated. Samples were collected bimonthly from September 2008 to March 2009 with a Van Dorn bottle at two depths (surface and bottom) (n = 16). Water temperature was greater than 22.50 °C; pH values ranged from 6.09 to 8.42; and nitrogen-phosphorus ratios were low (0.11-1.46). The low N:P ratios indicated high phosphorus input, and an eutrophic to hypereutrophic condition in the reservoir. A significant positive correlation of spatial and temporal distribution of C. raciborskii with M. panniformis was observed. Canonical correlation analysis (CCA) results revealed significant association of the biomass of most cyanobacterial species with temperature and nutrients concentration. However, these factors did not explain the co-occurrence of C. raciborskii and M. panniformis. On the other hand, morphological and physiological adaptations such as the possession of aerotopes and production of mucilage, and co-operation between the two species permitted niche overlap, and consequently the co-occurrence of C. raciborskii and M. panniformis in Mundaú reservoir.