The global carbonate cycle has been controlled and maintained by life processes for at least 3.5 billion years. Within the exogenic carbonate cycle and in very different environments cyanobacteria appear in ‘key positions’ in that they actively and passively influence carbonate cycling. In the carbonate cycle, cyanobacteria play an important and sometimes decisive role. Cycling of carbon and carbonate is linked to biological processes. Some build up specific carbonate structures, some destroy carbonate substrates and others do both simultaneously. All these processes take place from the high mountains down to the sea in various terrestrial and freshwater as well as marine environments. The photosynthetic activity of cyanobacteria, their extracellular polymeric substances and possibly also their adherent heterotrophic bacteria are responsible for the construction of various carbonate structures and the ability to penetrate carbonate material. Boring activity of euendoliths results in biological corrosion and disintegration of carbonate surfaces. Grazing organisms on carbonate surfaces colonized by epi- and endolithic cyanobacteria produce specific biokarst forms and specific grains which can contribute to nearshore sedimentation. Biological corrosion and abrasion together constitute bioerosion. The results of all these processes are calcareous crusts, typical traces and biokarst forms which in many cases have a high fossilization potential, and therefore can be powerful ecological, palaeoecological and facies indicators in recent as well as in fossil environments.