The formations underlying the Neogene infill of the Vienna Basin are still poorly documented. Until now correlation of subsurface lithostratigraphic units with those of the Rhenodanubian nappe system and the Magura nappe system, outcropping at the basin margins, has been based on extrapolations. A recent drilling campaign in the Bernhardsthal oil field of the northern Vienna Basin in Austria reached the pre-Neogene basement and provided cuttings for biostratigraphic and paleoecological analyses. Based on these data, acquired by using detailed micro- and nanno-paleontological analyses, a Lutetian age (middle Eocene) and a bathyal depositional environment for the Flysch of the Harrersdorf Unit was documented. The lithological similarity of the drilling with the Steinberg Flysch Formation of the Greifenstein Nappe and its Lutetian age suggests, that the middle Eocene part of the Harrersdorf Unit represents a continuation of the Greifenstein Nappe of the Rhenodanubian Flysch, rather than a frontal part of the Rača Nappe of the Magura Flysch as previously thought.