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The ability to form biofilms is a functional trait shared by many bacterial species. Biofilms provide bacteria a sheltered environment where the nutrients and oxygen gradients create a heterogeneous matrix and promote cells to differentiate their metabolism and functions according to the position they occupy inside the matrix. Species of the Microcystis genus are among the most common bloom-forming cyanobacteria. They are unicellular microorganisms able to form colonies and to reach high biomass during blooms in lakes, reservoirs and estuaries worldwide. Colonial lifestyle provides several advantages under stressing conditions, including adaptation to different light intensities, protection from toxic substances and grazing, while allowing them to grow when the nutrient supply is low. Although the biology, ecology and colony formation have been extensively recognized in Microcystis spp., the analysis of the progression from unicellular to multicellular phases in this cyanobacterium have been always addressed as individual phenotypic plasticity and rarely as a multi-specific community of interrelated microorganisms. Here, we re-interpreted the evidence coming from different studies about the Microcystis lifestyle and propose a new way to analyze the available information about this cyanobacterial group. We specifically address the characteristics shared by bacterial biofilms and Microcystis colonies and suggest that the morphological changes from single cells to colonies are due to a cascade of events leading to the formation of a multi-specific biofilm. Studying the formation of colonies using this framework would help to better understand the life cycle of Microcystis, its functional relationship with the associated microbiome and the factors triggering microcystin production, helping to design strategies for prevention and control of the blooms caused by these organisms. Taking into account the biology and the ecological strategies of Microcystis, a conceptual model of emergence and decay of these floating multi-specific biofilms is proposed.