The biostratigraphy and paleoecology of the Middle Miocene, Lower Badenian deposits were studied in two boreholes (Ivan-1 and Vranovice-1) situated in the southern part of the Carpathian Foredeep, Czech Republic. Planktonic foraminifers document the M5b Zone of Berggren et al. (1995). Presence of Uvigerina macrocarinata Papp et Turnovsky and Praeorbulina glomerosa circularis (Blow) indicates “Lower Lagenid Zone” sensu Grill (1941). Calcareous nannofossils with Helicosphaera waltrans, H. walbersdorfensis and Sphenolithus heteromorphus give evidence for the NN5 Zone of calcareous nanoplankton (Martini 1971). Quickly changeable paleoenvironment, especially sea-level fluctuation and non-stable conditions are documented by five types of microfauna: 1. shallow-water foraminifers accompanied by fragments of molluscs and bryozoans — shallow sublittoral (infralittoral), 2. joint occurrence of agglutinated and calcareous benthic foraminifers — circalittoral to upper bathyal, 3. euryoxybiont foraminifers indicate low oxygen content in bottom water of the deeper sublittoral (circalittoral), 4. dominance of planktonic foraminifers with pyritized tests — low oxygen sea, circalittoral to upper bathyal, 5. mixed assemblages of shallow- and deep-water foraminifers document slumps. Generally, relatively shallow epicontinental sea of normal salinity with nutrient supply is supported by coastal nannoflora with higher numbers of Reticulofenestra minuta, Coccolithus pelagicus, and helicosphers. Low abundances of sphenoliths and scarce occurrence of discoasters may imply cooler surface waters. High numbers of reworked nannofossils reflect transgression.