Aim Empirical studies have often reported parallel patterns of genetic and species diversity, but the strength and generality of this association, as well as its origin, are still debated. Particularly in human-dominated landscapes with complex histories of land use histories, more complicated and partly diverging patterns have been observed. In this study, we examine whether species and genetic diversity correlate across grasslands with different levels of land use pressure and spatial differentiation in habitat quality and heterogeneity. Location We selected eight extensively used (grazed, unfertilized) dry grasslands and eight intensively used (mown, fertilized) hay meadows in southeastern Germany. Methods We used vegetation surveys and molecular markers of six widespread dry grassland and six hay meadow plant species to compare species and genetic alpha and beta diversity between the two grassland types. Results Species diversity patterns expectedly showed higher alpha diversity, stronger spatial structure and less turnover in dry grasslands than in hay meadows. Neither of the corresponding genetic diversity patterns showed the same significant trends. Main conclusion Our results question the idea that species and genetic diversity patterns will always show similar patterns. Likely, genetic and species diversity emerge partly from shared, partly from different processes, including the regional species pool, environmental heterogeneity, fragmentation and land use history. The practical conservation implication is that species and genetic diversity are not generally interchangeable. Looking at species and genetic patterns together, however, may eventually lead to a better understanding of the complex processes that shape the structure and dynamics of ecological communities.