The phytogeographical affinities of Corsica, Sardinia, Sicily, Crete, the Maltese and the Balearic Islands are analysed on the basis of the chorological information in the Atlas Florae Europaeae 1–13. Data for 1109 indigenous phanerogam species were used for the production of a similarity matrix and taxon richness maps for each island, showing the representation of its flora in Europe. Jaccard's similarity index values of each island and related mainland areas show a strong floristic similarity between the large W Mediterranean islands Corsica, Sardinia and Sicily, and parts of their adjacent mainland, which reflects a common geological history. The maps show that the Balearic Islands have many species in common with Malta, which depends on the prevailing pan-Mediterranean element. Many Sicilian taxa show up in the Balkans, while many species of (the mountains of) Corsica, Sicily and to a lesser extent of Sardinia appear in Central Europe. Such an element is absent in Crete, Malta and the Balearic Islands. Crete deviates widely from the other investigated areas as it has many species in common with the Cyclades and mainland Greece, but less so with the Balkans.