The distributional range of alpine plants experienced dramatic changes during the Quaternary ice ages. These changes offer many opportunities for studying the impact of habitat contraction and fragmentation on both species and genetic diversity. Here, we examined the amplified fragment length polymorphism-based genetic diversity in the sedge Carex curvula All. in relation to the species diversity of siliceous European alpine grasslands in which the sedge is dominant. We found no relationship or even a negative relationship between genetic and species diversity indices. Local species richness was associated with the regional pool size of siliceous alpine species, which was itself dependent on the extant area of suitable habitats for these species. Genetic diversity of C. curvula was primarily shaped by the presumed location of glacial refugia and the routes of post-glacial colonization. We conclude that the two levels of diversity are not positively correlated because genotypes and species do not respond similarly to the spatial dynamics of suitable habitats induced by Quaternary temperature changes.