A synthesis of available data on the morphological diversity of polykrikoid dinoflagellates allowed us to formulate a hypothesis of relationships that help explain character evolution within the group. Phylogenetic analyses of new SSU rDNA sequences from Pheopolykrikos beauchampii Chatton, Polykrikos kofoidii Chatton, and Polykrikos lebourae Herdman helped refine this hypothetical framework. Our results demonstrated that ''pseudocolonies'' in dinoflagellates evolved convergently at least three times independently from different Gymnodinium-like ancestors: once in haplozoans; once in Ph. beauchampii; and at least once within a lineage containing Ph. hartmannii, P. kofoidii, and P. lebourae. The Gymnodiniales sensu stricto was strongly supported by the data, and the type species for the genus, namely Gymnodinium fuscum (Ehrenb.) F. Stein, formed the nearest sister lineage to a well-supported Polykrikos clade. The best synapomorphy for the Polykrikos clade was the presence of two nuclei irrespective of zooid number. Two unidentified Gymnodinium species formed the nearest sister clade to Ph. beauchampii, which has four nuclei and four zooids per pseudocolony. The chain-forming dinoflagellate G. catenatum L. W. Graham branched closely to the clade containing all members of Polykrikos and Pheopolykrikos, suggesting that an ancestral capacity toward chain formation existed before the evolution of pseudocolonies in this group. Our results also clarified the phylogenetic significance of nematocysts, ocelloids, and photosynthesis in reconstructing the evolution of polykrikoids and warnowiids. The molecular phylogenies exposed taxonomic problems associated with Polykrikos, Pheopolykrikos, and Gymnodinium, and suggested that a revision for some of these genera is warranted.The dinoflagellate genus Polykrikos was erected by Bütschli (1873), with the type species P. schwartzii Bütschli. The most distinctive feature of this athecate genus is the formation of multinucleated pseudocolonies comprised of an even number of zooids that are otherwise similar in morphology to individual dinoflagellates in external view. However, despite every zooid having its own cingulum and pair of flagella, the zooid sulci are fused together. A pseudocolony often has half the number of nuclei because it has zooids. Trichocysts, nematocysts, taeniocysts, mucocysts, and plastids have all been reported from different members within the group. The genus currently comprises four species: P. schwartzii, P. kofoidii, P. lebourae, and P. grassei Lecal. The first three species are relatively well described and distinguishable from one another (