Within the last decades phenotypic analyses and molecular marker methods have widely found their application in studies on toxigenic microalgae at the inter- and intra-species level. Molecular phylogenies and clock methods have been used to test hypotheses on the order of lineage splitting and their dating, respectively. Toxin profiles and population genetic markers have been used to study differentiation of populations at different levels with respect to temporal and geographical scale and/or evolutionary organization. Interpretation of data, hitherto, mainly focused on the characterization of species specific traits and the development of particular models for the evolutionary histories of the species under study. However, taken together these data on biogeographic structures at different spatial and organizational scales comprises a sound basis for comparative analyses with generalized research questions: Which are the valid speciation concepts (e.g., allopatric, sympatric and parapatric speciation) in different groups of planktonic microalgae? How can causes of recent geographic range expansions of toxigenic microalgae (e.g., by human-mediated dispersal or as consequences of environmental disturbances and climate change) be distinguished? The aim of the presented meta-analysis is to reveal what patterns emerge from a comparative approach at different scales of organization of evolutionary units. Furthermore, hypotheses regarding the dependency of the emergent structures on phylogenetically determined traits (e.g., life history traits such as sexually produced resting cysts) are tested. Besides new insights on evolutionary communalities and divergences among lineages of toxigenic microalgae, the results of this study reveal, where more research is needed to produce a fine-grained picture of the evolution of toxigenic microalgae.