The recent increase in the availability of large vegetation-plot databases has created unprecedented opportunities for analysing and explaining patterns of fine-scale plant species richness across large areas and for individual habitat types. Here we demonstrate how these data can be used to (1) prepare country-wide high-resolution maps of species richness and identify national diversity hotspots for grassland and forest vegetation; (2) compare diversity patterns of all, native, alien and Red List species; and (3) identify potential environmental drivers of these patterns. At the same time we examine and quantify the stability of predicted species-richness patterns with respect to the most common biases that are inherent to large vegetation-plot databases. Vegetation-plot records were obtained from the Czech National Phytosociological Database and the Random Forest method was used to map fine-scale spatial diversity patterns of all, native, alien and Red List vascular plant species, separately for grasslands and forests across the Czech Republic. The stability of the predicted species-richness patterns was tested using differently resampled datasets in which we either reduced or increased local oversampling and preferential sampling of more species-rich communities. Models for grassland and forest vegetation explained 40–65% of variation in fine-scale species richness. Spatial patterns of all and native species richness differed considerably between grasslands and forests, whereas alien and Red List species showed a higher congruence between these two vegetation types. Patterns of modelled species richness were highly stable with respect to all resampling strategies applied to the initial datasets. We conclude that vegetation-plot databases are a valuable source of data for high-resolution mapping of the plant species richness of different vegetation types and species groups, because each of them can exhibit a different diversity pattern. The resulting maps provide robust representation of the spatial patterns of fine-scale species richness and can be used both for testing scientific hypotheses about the controls of diversity patterns and for conservation planning.