Abstract The Pannonian Basin system provides sufficient data to study local and regional vegetation in the context of palaeoclimate and palaeogeography. The present study attempts to make use of the latest results in stratigraphy and track vegetation change throughout the Late Miocene. Vegetation layers are reconstructed for five time slices, from 10.8 Ma to 6.5 Ma, and placed in a palaeogeographic context. Plant functional types and their distribution, frequently applied in ecological studies and biome modelling, serve as a tool for reconstructing palaeovegetation units. A classification system is introduced considering non-zonal elements as well, in order to represent the Neogene floral record. The PFT spectra obtained from fossil leaf assemblages indicate the presence of mainly broadleaved deciduous vegetation throughout the regarded time span, with variable diversities of conifers and broadleaved evergreen vegetation components. During the Late Miocene, the lowland vegetation of the Pannonian realm seemed to be more homogeneous than reported in other reconstructions, which is in line with the persistence of overall warm and humid climate conditions. The existence of distinctly dry periods as partly suggested by other proxies is not supported. At the same time, data suggest the coeval declining trend of the broadleaved evergreen component in the study area, and its final complete disappearance from the north of the Pannonian Basin. In the younger time slices, constantly humid conditions might have existed along the northern border of the lake, possibly connected to uplift pulses of the Alps and Carpathians.