Two separate taxonomic traditions have arisen in dinoflagellates at the generic level and below: one centred on the living motile cell but potentially incorporating all aspects of the biology, and the other based exclusively on resting cyst morphology including the fossil record. Where a cyst has been described and named as a fossil and subsequently shown through life-cycle observations to be equivalent to a named living species, the cyst morphotype may then bear two names. This dual nomenclature is supported for all algae (diatoms excepted) by the International Code of Nomenclature for Algae, Fungi and Plants (ICN) through Articles 1.2, 11.1, and 11.7 (Head, M.J. et al., 2016, Taxon 65: 902– 903). The ICN acknowledges that a fossil-taxon (having a fossil as its type) is conceptually distinct from its living (non-fossil) counterpart, and that equivalency need not mean synonymy. This distinction reflects the different species concepts involved, based on different stages of the same life cycle, and acknowledges that cyst morphology alone retrieves only limited genetic information from the fossil record. While cyst-based taxonomy strives to reflect evolution, there is a long observed mismatch between fossil-defined genera and the genera of living equivalents. Molecular phylogenies from living material now expose these discrepancies and others with new clarity. This requires the reassessment of our current taxonomic schemes if they are to be more reflective of evolution, although any major nomenclatural changes should be balanced against the value of stability in connecting living dinoflagellates to their fossil lineages.