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Loss of natural habitat is one of the major threats for biodiversity worldwide. Habitat conversion not only changes diversity and species composition locally (alpha diversity) but might also lead to large-scale homogenization of species communities and decrease in regional species richness (gamma diversity). We investigated the effect of farmland conversion on amphibian communities in Rwanda and compared local and regional (country-wide) taxonomic, functional and phylogenetic diversity between natural and farmland sites (agricultural marais). Alpha diversity was higher in the disturbed farmland than in natural sites. However, species turnover among farmland sites was much lower than among natural sites, resulting in highly homogenized amphibian communities and much lower country-wide taxonomic, functional and phylogenetic gamma diversity in farmland compared to natural sites. The few frog species found in farmland were mostly disturbance-tolerant species that are widespread in Eastern Africa and beyond. In contrast, most of the regionally endemic frog species that make this region a continent-scale hotspot of amphibian diversity were found only in the natural habitats. Ongoing farmland conversion might lead to a loss of regional endemism and a widespread homogenization of species communities across sub-Saharan Africa.