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The native flora and a number of environmental factors were recorded for twenty islands in the eastern Aegean archipelago (Greece) in order to study the patterns of native and endemic plant species diversity as well as the effects of environmental factors in shaping these patterns at different levels of endemism. Stepwise regressions were used to test the effects of these factors on species richness of native and especially of endemic plants, at local scales. The performance of the Choros model was also compared with the separate effects of area and habitat diversity using simple linear regressions. The residuals from the species–area functions of native and endemic species were used as indices of relative island richness. Out of the 2238 species and subspecies recorded in total, 302 taxa (13.4%) are endemics (either single island endemics or endemic at a broader scale, namely Aegean, Greek-Aegean, or …