Ionian archipelago is the second largest Greek archipelago after the Aegean, but the factors driving plant species diversity in the Ionian Islands are still vague. We used stepwise multiple regressions to investigate the factors affecting plant species diversity in 17 Ionian Islands. Generalized Dissimilarity Modelling was applied to examine variation in the magnitude and rate of species turnover along environmental gradients, as well as to assess the relative importance of geographical and climatic factors in explaining species turnover. The values of the residuals from the ISAR log10‐transfomed models of native and endemic taxa were used as a measure of island floristic diversity. Area was confirmed to be the most powerful single explanatory predictor of all diversity metrics. Mean annual precipitation and temperature, as well as shortest distance to the nearest island are also significant predictors of vascular plant diversity. The island of Kalamos constitutes an important plant diversity hotspot in the Ionian archipelago. The recent formation of the islands, the close proximity to the mainland source and the reduced dispersal filtering of the Ionian archipelago resulted in islands with a flora principally comprising common species and a low proportion of endemics. Small islands keep a key role in conservation of plant priority sites.