Cyanobacteria constitute pioneer colonizer of specific environments whom settlement in new biotopes precedes the establishment of composite microbial consortia. Some heterotrophic bacteria constitute cyanobacterial partners that are considered as their cyanosphere, being potentially involved in mutualistic relationships through exchange and recycling of key nutrients, and sharing of common goods. Several non-axenic cyanobacterial strains have been recently isolated along with their associated cyanosphere from the thermal mud of Balaruc-les-Bains (France) and the biofilms of the retention basin where they develop. The community structure and relationships among members of the isolated cyanobacterial strains were characterized using a metagenomic approach combined with taxonomic and microscopic description of the microbial consortia. Results provide insights into the potential role and metabolic capabilities of microorganisms of thermal mud-associated cyanobacterial biofilms. Thus, the physical proximity, host-specificity and complimentary functions advocate for their complementarity between cyanobacteria and their associated microbiota. Besides these findings, our results also highlight the great influence of the reference protein database chosen when performing functional annotation of the metagenomes from organisms of the cyanosphere and the difficulty of selecting one unique database that appropriately cover both autotroph and heterotroph metabolic specificities.