Microrganisms such as cyanobacteria have been often considered as exhibiting wide distribution mainly driven by environmental heterogeneity. Recently, however, new findings have evoked the role of previously neglected processes, such as dispersal limitation, determining the distribution of a wide range of microorganisms, including cyanobacteria. Here, we reviewed the biogeographic patterns of cyanobacteria with focus on molecular data and the evidences from the published literature for the processes driving these patterns. Also, considerations are made about concept of species, discordances in the taxonomic concepts, and level of taxonomic resolution, and how these affect the biogeographic study of cyanobacteria. From a overview, it can be observed that both environmental and historical factors are important to structure cyanobacteria diversity across time and space. Moreover, different species may exhibit significant differences in their distribution patterns, from possibly cosmopolitan species to other endemic species. However, distribution patterns are closely dependent on the concept of species, besides the taxonomic resolution, spatial and environmental scales, and the biases of the molecular methodologies applied in the studies. Thus, efforts to broaden sampling and sequencing of unknown and less-known species, as well as geographic regions and habitats poorly exploited, are crucial for a better understanding of cyanobacteria biogeography.