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Background: Greece has two island archipelagos, the Aegean and the Ionian, which host a rich array of plants and wildlife, particularly endemic and threatened plant species. Despite the long history of island biogeographic studies in the Aegean, similar studies in the Ionian remain limited, with the two island archipelagos rarely being compared. Results: The Aegean and Ionian archipelagos share many features, especially regarding total plant diversity, but exhibit different patterns of endemism. For instance, when considering similarly sized islands, those in the Ionian host as many as, if not more, species compared to the Aegean. In contrast, the Ionian Islands are poor in endemics (particularly narrow range endemics, such as single island or regional endemics) and threatened taxa, compared to the Aegean Islands. In the Ionian, endemics only persist on the largest islands, and form a very small proportion of the species pool, compared to the Aegean archipelago. Conclusions: The lack of endemism might be attributed to the more recent separation of the Ionian Islands from the mainland and the shorter distance separating them from the mainland. In addition, the Ionian Islands receive higher levels of precipitation and are typically covered by denser and higher vegetation than the Aegean Islands. These conditions favour greater total species richness, but tend to lead to higher numbers of common species compared to threatened and endemic taxa. This study demonstrates that both isolation and precipitation serve as biodiversity drivers, influencing plant species diversity and endemism patterns, of the two Greek archipelagos. [ABSTRACT FROM AUTHOR]