The geology of the earth has shown profound changes in the position, connectivity and topography of continents during the last 100 Myr, which could have shaped the diversification of lineages and thus the current distribution of biodiversity. Here, we evaluate the association between plate tectonics and the current location of hotspots of endemic richness across the globe. We used palaeogeographies in a model that quantifies, through time and for each geographic cell, the potential dispersal between disconnected habitat areas. We expected that rare dispersal events across barriers of unsuitable habitat allow species colonization, but a subsequent absence of gene flow could lead to in situ speciation. We evaluated whether this process could pinpoint the locations of hotspots of endemic richness computed from the ranges of 181 603 species across 14 taxonomic groups. The significant spatial congruence between the model and the endemic richness of several clades provides evidence of the contribution of plate tectonics in shaping global biodiversity gradients. The signal of plate tectonics was independent from those of the Quaternary glaciation, topographical heterogeneity and contemporary productivity and was stronger for terrestrial than freshwater and marine taxa. Regions with high tectonic complexity, predominantly located at the confluence of major lithospheric plates such as the Mediterranean basin, Mesoamerica, Madagascar and South East Asia, probably provided favourable circumstances for allopatric speciation and the emergence of new species across straits. Further efforts should be made to disentangle the effect of past diversification relative to current ecological interactions in shaping global patterns in species diversity.