© 2017 The Author(s). Although environmental changes and evolution of life are potentially recorded via microbial carbonates, including laminated stromatolites and clotted thrombolites, factors controlling their fabric are still a matter of controversy. Herein, we report that the exopolymer properties of different cyanobacterial taxa primarily control the microbial carbonates fabrics in modern examples. This study shows that the calcite encrustation of filamentous Phormidium sp. secreting acidic exopolymers forms the laminated fabric of stromatolites, whereas the encrustation of coccoid Coelosphaeriopsis sp. secreting acidic exopolymers and poor calcification of filamentous Leptolyngbya sp. secreting non-acidic exopolymers form peloids and fenestral structures, respectively, i.e. the clotted fabric of thrombolites. Based on these findings, we suggest that the rise and decline of cyanobacteria possessing different exopolymer properties caused the expansion of thrombolites around the Proterozoic/Cambrian boundary.