In contrast with macroorganisms, whose geographical ranges are typically restricted, many microbial species appear to have cosmopolitan distributions. This observation has been explained as a consequence of ubiquitous dispersal caused by the enormous population sizes of microbial species. Recently, this "everything is everywhere, but, the environment selects" theory has been challenged by the detection of considerable regional genetic variability within microbial morphospecies. We demonstrate that, contrary to what is expected under ubiquitous dispersal, evidence of regional-scale metacommunity processes can be detected in microbial morphospecies. Our results imply that the microbial and macrobial world are structured by analogous processes.