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: To investigate the factors that affect plant species richness and identify plant diversity hotspots in the SAVA and other central Aegean islands. Methods: We used stepwise multiple regression to test the relationship between a number of 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: The area was confirmed to be 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 measures. Anafi, Amorgos and Folegandros were found to be endemic plant diversity hotspots. Conclusions: We have demonstrated that geodiversity is 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.