Background: The South Aegean Volcanic Arc (SAVA), one of the most notable geological structures of the Mediterranean Sea, is floristically well-known. Nevertheless, the factors that contribute to shaping the plant species richness of the SAVA remain unclear. Aims: Investigate factors that affect plant species richness and identify plant diversity hotspots in the SAVA and other central Aegean Islands. Methods: We used stepwise multiple regressions to test the relationship between several environmental factors and plant species richness in the SAVA, as well as the residuals from the species-area linear regressions of native, Greek and Cycladian endemic taxa as indicators of relative species richness. Results: Area was confirmed as the most powerful single explanatory variable of island species richness, while geodiversity, maximum elevation and mean annual precipitation explained a large proportion of variance for almost all the species richness metrics. Anafi, Amorgos and Folegandros were found to be endemic plant diversity hotspots. Conclusions: We demonstrated that geodiversity was an important factor in shaping plant species diversity in the Cyclades, while mean annual precipitation, human population density and maximum elevation were significant predictors of the Greek endemics present in the Cyclades. Finally, Anafi was found to be a plant diversity hotspot in the South Aegean Sea.