The beaches of the North Sea barrier island Schiermonnikoog (The Netherlands) are covered by microbial mats. Five types of microbial mats were distinguished based on a variety of characteristics, located along a transect perpendicular to the coast. Biomass abundance and composition of the microbial community were analyzed in these mats using pigments and phospholipid-derived fatty acids (PLFA) as biomarkers. Biomass per gram sediment increased more than six-fold from the mats at the low water mark to mats found at the edge of the dunes. Microscopic analysis revealed that the increase in biomass was accompanied by a change in species composition. Pigment- and PLFA composition reflected the changes in species composition. The PLFA data could be used to estimate the relative group abundance using the matrix factorization program CHEMTAX., whereas the pigment data were found not to be suitable for this purpose.