The seasonal succession of brackish microphytobenthos (consisting of diatoms and cyanobacteria) was studied at a wind flat at the southern Baltic Sea coast. Wind flats are coastal zones with a high degree of exposition becoming flooded irregularly as a function of sea levels, prevailing wind direction and speed. These extreme environmental conditions favour the formation of laminated microbial mats similar to those in tidal flats. Special attention was paid to the comparison of diatom compositions in a laminated microbial mat as a relatively steady biocoenosis, and compositions in sediment without a mat, probably a more disturbed area. Therefore, monthly sediment samples from March to November 2002 were examined at two adjacent stations (reference station without mat, microbial mat station). Biomass (chlorophyll a content), cyanobacterial and diatom abundance, species composition and diversity were determined. The main mat forming cyanobacteria were Microcoleus chthonoplastes and Lyngbya aestuarii. The laminated mat exhibited a larger total biomass from spring on, while diatoms at the reference station accumulated relatively more biomass until late summer. 93 diatom taxa were identified in total. The species compositions at both stations were similar compared to those inhabiting other sandy and shallow water areas of the Baltic Sea. However, in the mat inhabiting diatom community lower relative abundances of very small species (<15 μm) were determined. In contrast to tidal flats, diatoms of the wind flat were found in much deeper zones of the mat (down to 1 cm), which may contribute to less anoxic conditions. This occurrence may be influenced by the specific sediment features, such as larger sand grain sizes. Species numbers were moderate within a given sample, indicating that environmental conditions in wind flats are extreme and outside of the tolerance limits of many species. On the other hand, the Shannon–Weaver index was comparably high due to its evenness component, so that disturbances may have been too frequent to establish climax communities, i.e. supporting few strongly dominant species. Nevertheless, the total biomass accumulated in the range of many other microphytobenthos communities in spite of extreme conditions hinting on good adaptation and protection capabilities, e.g. mucous material with high water retention potential.