Lower Messinian stromatolites of the Calcare di Base Formation at Sutera in Sicily record periods of low sea-level, strong evaporation and elevated salinity, thought to be associated with the onset of the Messinian Salinity Crisis. Overlying aragonitic limestones were precipitated in normal to slightly evaporative conditions, occasionally influenced by an influx of meteoric water. Evidence of bacterial involvement in carbonate formation is recorded in three dolomite-rich stromatolite beds in the lower portion of the section that contain low domes with irregular crinkly millimetre-scale lamination and small fenestrae. The dominant microfabrics are: (i) peloidal and clotted dolomicrite with calcite-filled fenestrae; (ii) dolomicrite with bacterium-like filaments and pores partially filled by calcite or black amorphous matter; and (iii) micrite in which fenestrae alternate with dark thin wispy micrite. The filaments resemble Beggiatoa-like sulphur bacteria. Under scanning electron microscopy, the filaments consist of spherical aggregates of dolomite, interpreted to result from calcification of bacterial microcolonies. The dolomite crystals are commonly arranged as rounded grains that appear to be incorporated or absorbed into developing crystal faces. Biofilm-like remains occur in voids between the filaments. The dolomite consistently shows negative δ13C values (down to −11·3‰) and very positive δ18O (mean value 7·9‰) that suggest formation as primary precipitate with a substantial contribution of organic CO2. Very negative δ13C values (down to −31·6‰) of early diagenetic calcite associated with the dolomite suggest contribution of CO2 originating by anaerobic methane oxidation. The shale-normalized rare earth element patterns of Sutera stromatolites show features similar to those in present-day microbial mats with enrichment in light rare earth elements, and M-type tetrad effects (enrichment around Pr coupled to a decline around Nd and a peak around Sm and Eu). Taken together, the petrography and geochemistry of the Sutera stromatolites provide diverse and compelling evidence for microbial influence on carbonate precipitation.