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Abstract Aim The aim of this study is to explore the interrelationships between island area, species number and habitat diversity in two archipelago areas. Location The study areas, Brunskär and Getskär, are located in an archipelago in south-western Finland. Methods The study areas, 82 islands in Brunskär and 78 in Getskär, were classified into nine habitat types based on land cover. In the Brunskär area, the flora (351 species) was surveyed separately for each individual habitat on the islands. In the Getskär area, the flora (302 species) was surveyed on a whole-island basis. We used standard techniques to analyse the species–area relationship on a whole-island and a habitat level. We also tested our data for the small island effect (SIE) using breakpoint and path analysis models. Results Species richness was significantly associated with both island area and habitat diversity. Vegetated area in particular, defined as island area with the rock habitat subtracted, proved to be a strong predictor of species richness. Species number had a greater association with island area multiplied by the number of habitats than with island area or habitat number separately. The tests for a SIE in the species–area relationship showed the existence of a SIE in one of the island groups. No SIE could be detected for the species–vegetated area relationship in either of the island groups. The strength of the species–area relationship differed considerably between the habitats. Main conclusions The general principles of island biogeography apply well to the 160 islands in this study. Vascular plant diversity for small islands is strongly influenced by physiographic factors. For the small islands with thin and varying soil cover, vegetated area was the most powerful predictor of species richness. The species–area curves of various habitats showed large variations, suggesting that the measurement of habitat areas and establishment of habitat-based species lists are needed to better understand species richness on islands. We found some evidence of a SIE, but it is debatable whether this is a ‘true’ SIE or a soil cover/habitat characteristics feature.