Modern dolomite stromatolites were previously described in the hypersaline Petukhovskoe Soda Lake (Southwestern Siberia, Russia). Exopolysaccharides (EPSs) secreted by phototrophic communities have previously been shown to play a crucial role in their formation. In the current study, using transmission electron microscopy (TEM) with energy dispersive X-ray (EDX) spectral microanalysis, we demonstrate that clay minerals also play a significant role in the dolomitization of Ca-Mg carbonates in this lake. The lake is characterized by the development of phototrophic communities, whose huge biomass accumulates near the shoreline and gradually dries out, finally forming cavernous crusts that later become stromatolites. Three samples (S1, S2, and S3) were collected simultaneously in the littoral at different distances from the water and represent successive stages (from S1 to S3) of phototrophic biomass desiccation. TEM revealed ubiquitous clay minerals (consistent with montmorillonite composition) in all samples, which were represented by free clay particles, fine clay particles surrounding cell walls, and a completely interstitial clay-EPS matrix. Carbonate crystals of varying sizes were embedded in this matrix. IR spectroscopy indicates a transition from predominantly high-Mg calcite in S1 to a dolomite composition in S3. Consistently, TEM-EDX analysis of 130 points revealed a statistically significant decrease in the average Mg/Ca (atomic %) ratio in carbonate crystals from 4.8±2.9 (S1) to 2.8±1.2 (S2) and 1.3±0.2 (S3), while the opposite trend was observed in the Mg/Si ratio: 0.7±0.1 (S1), 1.1±0.3 (S2), and 2.0±1.2 (S3). These ratios in clays did not change significantly. The 3-5-fold excess of Mg over Ca at the analyzed points in carbonate crystals in S1 and S2 indicates that Mg may have originally been associated with clay minerals, which act as Mg donors for incorporation into the Ca-Mg carbonate crystal lattice. This research was funded by the Ministry of Science and Higher Education of the Russian Federation.