During the Middle Miocene, an extensive lake district existed along the southern margin of today’s Swabian Alb (Baden–Württemberg). Sediments include a wide range from marls to pure carbonates of lacustrine and palustrine origin that contain microbialites studied here. These sediments are part of the Obere Süßwassermolasse known as Silvana Beds. Macroscopically the studied microbialites show a distinctive layering with an alternation of whitish and tan-colored layers. Petrographic thin sections as well as SEM studies reveal a microstructure of the microbialites comprising an unbranched filament zone formed by erect and parallel calcified filaments as well as a zone of branching filaments forming shrubs of the Dichothrix morphotype. We define two patterns of mineralization for the studied microbialites: (1) shape-retentive mineralization: successive carbonate precipitation along the filament surface. (2) shape-obscuring mineralization: clusters of clotted micritic precipitates along and within the vicinity of micro-sparitic tubules that probably represent remains of the former cyanobacterial sheaths.