Benthic cyanobacterial blooms are increasing worldwide and can be harmful to human and animal health if they contain toxin-producing species. Microbial interactions are important in the formation of benthic biofilms and can lead to increased dominance and/or toxin production of one or few taxa. This study investigated how microbial interactions contribute to proliferation of benthic blooms dominated by the neurotoxin-producing Phormidium autumnale. Following a rainfall event that cleared the substrate, biofilm succession was characterised at a site on the Hutt River (New Zealand) by sampling every 2-3 days over 32 days. A combination of morphological and molecular community analyses (automated ribosomal intergenic spacer analysis and Illumina™ MiSeq sequencing) identified three distinct phases of succession in both the micro-algal and bacterial communities within P. autumnale-dominated biofilms. Bacterial composition shifted between the phases, and these changes occurred several days before those of the micro-algal community. Alphaproteobacteria and Betaproteobacteria dominate in the early phase; Alphaproteobacteria, Betaproteobacteria, Sphingobacteria and Flavobacteria in the mid-phase; and Sphingobacteria and Flavobacteria in the late phase. Collectively, the results suggest that succession is driven by bacteria in the early stages but becomes dependent on micro-algae in the mid- and late stages of biofilm formation.