We empirically assessed the long-term changes in the rare species assemblage of a Mediterranean flora, in terms of species life history traits, niche and biogeographic features, and taxonomic groups. We used a 115-year historical record of ca. 2100 plant species occurrences in a 6250 km2 region in Mediterranean France. Species were assigned to two classes of regional abundance for the years 1886 and 2001 (rare species, i.e. exhibiting one or two occurrences vs. nonrare species), and to three classes of abundance changes during 1886–2001 (decreasing/extinct, stable, increasing/immigrant). Then, we tested whether species regional abundance and species abundance change were related to their morphological and life-history traits (life form, perenniality, height, dispersal agent, pollination mode), niche and biogeographic features (habitat specialization, level of endemism, biogeographic origin) and taxonomic group. The regional assemblage of rare species was not biologically random and significantly changed between 1886 and 2001. Species classified as rare in 1886 had a significantly higher rate of extinction in the study region during 1886–2001. The highest rate of regression/extinction was found among hydrophyte and/or water-dispersed rare species, and among annual rare species. However, herbaceous perennial, tree and wind-dispersed rare species significantly increased in abundance during 1886–2001. Rare species with Eurosiberian distributions, occurring at the southern margin of their range in the study region, dramatically declined or went extinct in the region during 1886–2001; whereas rare species with Mediterranean affinities remained significantly stable. We also found strong evidence for taxonomic patterns in species abundance and abundance changes from 1886 to 2001. The long-term biological changes documented here in the rare species assemblage of a Mediterranean flora are consistent with the predicted consequences of climate and land use changes currently occurring in the Mediterranean Basin. With the potential decline or even extinction of entire taxa and the loss of southern ecotypes of widespread Eurosiberian species, both evolutionary history and speciation potential of the Mediterranean Region could be strongly altered in future decades.