Aim Assessing whether environmental and human factors influenced the spatial distribution and the dynamics of regionally rare plant species since the late nineteenth century, and whether these spatial and temporal patterns of rare species occurrences differ according to their chorology (level of endemism and biogeographic affinity). Location An area extending over 6250 km2 in the French Mediterranean Region. Methods We used two botanical surveys achieved in 1886 and in 2001, and considered species rare if occurring in only one or two sites in the study area. Each rare species was assigned to a group of endemism level (restricted endemic, non-endemic), and of biogeographic affinity (Mediterranean, South/Central European, Mountain, Eurosiberian). A 1 × 1 km grid was applied to the study zone. Generalized linear models were developed to study the spatial distribution and the fate of rare species occurrences (local extinction vs. local persistence between 1886 and 2001), as a function of environmental and human variables. Multivariate analyses were used to test whether the spatial distribution and the fate of rare species occurrences differed according to their chorology. Results In 2001, rare species as a whole tended to occur at higher altitude, in zones dominated by semi-natural open habitats, and where cultivated area had decreased in the last 30 years. Between 1886 and 2001, rare species were the most prone to local extinction in zones where human population density, cultivated area and livestock density had increased the most. Between 1886 and 2001, rare species had a higher probability of local persistence in zones of high altitude and steep slope, on basic bedrocks and with low cultivated area. Rare species with Mountain and Eurosiberian affinities occurred in marginal habitats in the study region, i.e. on gneiss-micaschist bedrocks and at high altitudes, whereas Mediterranean and South/Central European rare species occupied more varied environmental conditions. Between 1886 and 2001, Eurosiberian rare species showed high rates of local extinction whereas Mediterranean rare species had a significantly higher probability of local persistence. Restricted endemic species mostly occurred in zones of high slope, low human population density, and where cultivated area had decreased in the last 30 years. Occurrences of restricted endemics remained significantly stable between 1886 and 2001. Main conclusions Environmental and land-use changes that occurred over the twentieth century in the Mediterranean Basin had significant impacts on the spatial distribution and on the long-term dynamics of rare species occurrences. Urbanization and recent agriculture intensification, occurring mainly in coastal plains and littoral zones, caused most local extinctions of rare species from 1886 to 2001. Local populations of Eurosiberian species, which reach their range limits in marginal zones of the Mediterranean, also appear to be highly vulnerable. Conversely, most restricted endemic species occur in habitats with harsh topography and low human disturbance and have a higher potential of local persistence.