The island of Anafi, located in the southern Kiklades in Greece, constitutes together with the Santorini island group the central part of the South Aegean Volcanic Arc. The flora of Anafi consists of 635 taxa, 128 of which are under a protection status, 37 are Greek endemics and 181 are reported here for the first time. We show that Anafi has the highest percentage of Greek endemics in the South Aegean Volcanic Arc. The known distribution of the endemics Sedum littoreum var. creticum and Sternbergia greuteriana is expanded, being reported for the first time for the phytogeographical region of the Kiklades, and the indigenous presence of Phoenix theophrasti in Anafi is confirmed. Calculating the floristic cross-correlation between Anafi and the other parts of the South Aegean Volcanic Arc by means of Sψrensen’s index revealed that phytogeographical affinities are somewhat stronger to Milos than to the neighbouring Santorini.