The south-western part of the White Carpathians (Czech Republic, Slovakia) is known for its exceptional grassland diversity and occurrence of many species with disjunct distribution patterns, including isolated populations of continental forest-steppe species. The north-eastern part of the mountain range lacks many of these species and has clearly lower maxima of grassland species richness. While climatic and edaphic conditions of both regions largely overlap, specific environmental history has been hypothesized to explain the exceptional richness in the south-western part. We explored an entire-Holocene record (9650 BC onwards), the first one from the northeastern part, to find out whether differences in history may explain regional patterns of species rarity and richness. All available evidence confirmed an early post-Glacial expansion of broad-leaved trees, supporting the hypothesis on their glacial refugia in the Carpathians, as well as presence of closed-canopy forest well before the Neolithic. This environmental history was unfavourable for the survival of Early-Holocene forest-steppe species in the north-eastern White Carpathians and may explain the impoverished grassland flora compared to the south-western part. We conclude that contrasting Holocene histories may explain those patterns in species richness and distributions, which cannot be explained by recent environmental conditions alone.