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Some algal species have extended their native range. Problems in settling on a proper definition of 'alien' for microorganisms have made it difficult to unequivocally assess whether their spread was natural or resulted from human intervention. As direct evidence seems to be virtually non-existent, the only option is to rely on circumstantial evidence. In this paper, we discuss the expansion routes of three cyanobacteria species: Cylindrospermopsis raciborskii, Raphidiopsis mediterranea and Cuspidothrix issatschenkoi. We analyse the information available for these species, which are commonly regarded as alien, in order to establish the context in which the migration and evolution of these microorganisms should be understood, so that a proper assessment of their geographic expansion can be made. A more complete picture of the expansion and evolution of microorganisms must combine many types of information, including the history of local expansions, ecological ranges, and data from studies in morphology, ecology, genetics and paleolimnology.