Succession in bloom-forming cyanobacteria belonging to distant functional groups in freshwater ecosystems is currently an undescribed phenomenon. However in the Hammam Debagh reservoir (Algeria), P. rubescens and Microcystis sp. co-occur and sometimes proliferate. With the aim of identifying the main factors and processes involved in this unusual cohabitation, water samples were collected monthly from February 2013 to June 2015 at the subsurface at four sampling stations and along the entire water column at one sampling station. In addition, the composition of the cyanobacterial communities was estimated by Illumina sequencing of a 16S rRNA gene fragment from samples collected over one year (October 2013-November 2014). This molecular approach showed that the Hammam Debagh reservoir displays high species richness (89 species) but very low diversity due to the high dominance of Microcystis in this community. Furthermore, it appears that Planktothrix rubescens and Microcystis sp. coexisted (from September to January) but proliferated alternately (Spring 2015 for P. rubescens and Spring 2014 and Autumn 2014/2015 for Microcystis). The main factors and processes explaining these changes in bloom-forming species seem to be related to the variation in the depth of the lake during the mixing period and to the water temperatures during the winter prior to the bloom season in spring.