Data for manuscript "Holocene plant diversity dynamics shows a distinct biogeographical pattern in temperate Europe" by Roleček J., Abraham V., Vild O., Svitavská Svobodová H., Jamrichová E., Plesková Z., Pokorný P. & Kuneš P. Data originate from 18 sites in Czech and Slovak Republic. Original data and further metadata are stored in Czech Quaternary Palynological Database. Data presented here were adjusted by following procedure: Pollen counts of trees were adjusted (divided) by mean pollen productivity for North Hemisphere : Abies 6.88 Alnus 7.46 Betula 4.4 Carpinus betulus 4.52 Corylus 1.97 Fagus 1.96 Fraxinus excelsior-Typ 1.25 Juniperus 9.8 Picea 2.29 Pinus 10.47 Quercus 3.33 Tilia 1.17 Ulmus 7.32 and subsequently whole spectra were resampled for the same pollen sum (100 grains) in all depths and time windows (300 years). Resampling was done by function "spectra_to_target_sum" at https://github.com/vojtechabraham/pollen. See repository https://github.com/vojtechabraham/HolDivTempEur for the analysis presented in the paper.