This study aimed to estimate and explain the compositional differentiation and observed beta-diversity (partitioned as turnover and nestedness) patterns of woody species in Greece. Specifically, the 13 phytogeographical regions of Greece were compared at three taxonomic levels: family, genus, and (sub-) species. In Greece, 565 woody taxa have been identified, which are classified into 224 genera and 85 families. Phytogeographical regions were grouped according to their similarity in floristic composition using cluster analysis. Dominant beta diversity gradients were detected using Mantel directional correlation tests applied at the three taxonomic levels. The 13 phytogeographical regions formed three groups; namely, the northern, central, and southern (Aegean Islands) regions. The taxonomic variation among the phytogeographical regions at the species level was related to a gradient of richness of widespread taxa and Balkan endemic taxa. Analysis at the taxonomic levels of species and genus produced similar results, yet, at the family level, floristic differences were less pronounced, with phytogeographical regions being aggregated in two groups: the southernmost island regions versus all other regions. Beta diversity was higher along a northwestern to southeastern gradient, which was related to a dominant climatic gradient throughout Greece. The partitioning of beta diversity between neighboring phytogeographical regions showed that species turnover was the dominant component; yet, some phytogeographical regions (e.g., Kiklades) were characterized by high nestedness. In conclusion, analysis of woody taxa provides different insights regarding the floristic variation of phytogeographical regions.