In national conservation plans, it is necessary to comparatively assess species pools of different regions and monitor their changes over time. Two specific problems arise: i) species diversity must be standardized per area, because regions differ in size, and ii) the diversity measure should take into account how common or rare the species are on the regional scale. We used the rarefaction method combined with a fitting procedure to calculate the expected number of species E(S). The method takes into account the nonlinearity of species and area, as well as how common or rare each species is and allows analysis of species groups’ contribution to total species diversity. The slope parameter of the fitted power function is used as an indicator of species turnover, and thus, of β-diversity. For the analysis, Switzerland was divided into seven biogeographic regions (256–10 642 km2). The diversity of the total species pool and of six ecological species groups was investigated for each region. In every biogeographic region, we find the lowest species turnover in the fertilized meadow group, and the highest species turnover in the pioneer/weedy species and the mountain species groups pioneer/weedy. The results show that among Swiss regions, differences in E(S) are mainly due to the presence or absence of mountain species. Other species groups show a rather constant contribution to the regional species pools. We found the rarefaction method to be a very useful tool for assessing Swiss plant species diversity on a regional scale.