The Aegean archipelago is one of the largest archipelagos in the world and has long fascinated biogeographers due to its high environmental heterogeneity, complex palaeogeography, high diversity and endemism. In this study, prominence has been given to the plant diversity and biogeography of the Aegean area. After describing the phytogeographical aspects in the Aegean archipelago from the first division in phytogeographical areas, the current widely used subdivisions to the recent aspects of the Aegean phytogeographical classification, a synoptic analysis of the Aegean plant diversity is presented focusing on the Aegean endemics, the range-restricted plant taxa, the single island endemics, the protected plant taxa and the most Critically Endangered ones. Plant diversification and speciation in the Aegean and factors driving them, as revealed by molecular studies, are discussed briefly. The ruderal, alien and invasive plant taxa richness has also been mentioned. Emphasis is also given to small islands and islets plant species diversity. Factors affecting plant species richness in the Aegean, such as the long-lasting human presence, climate, area, elevation, habitat diversity, isolation, geological substrate and structure are discussed on the basis of different biogeographical studies concerning the Aegean area.