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There is a long-standing belief that microbial organisms have unlimited dispersal capabilities, are therefore ubiquitous, and show weak or absent latitudinal diversity gradients. In contrast, using a global freshwater diatom data set, we show that latitudinal gradients in local and regional genus richness are present and highly asymmetric between both hemispheres. Patterns in regional richness are explained by the degree of isolation of lake districts, while the number of locally coexisting diatom genera is highly constrained by the size of the regional diatom pool, habitat availability, and the connectivity between habitats within lake districts. At regional to global scales, historical factors explain significantly more of the observed geographic patterns in genus richness than do contemporary environmental conditions. Together, these results stress the importance of dispersal and migration in structuring diatom communities at regional to global scales. Our results are consistent with predictions from the theory of island biogeography and metacommunity concepts and likely underlie the strong provinciality and endemism observed in the relatively isolated diatom floras in the Southern Hemisphere.