Light and electron microscopy, nuclear-encoded LSU rDNA sequences, and pigment analyses were performed on five geographically separate isolates of Gymnodinium mikimotoi. The morphological variation between the isolates equals that found within the isolates. The nuclear-encoded LSU rDNA sequences were nearly identical in all isolates, and molecular analyses using maximum likelihood, parsimony, and neighbor joining showed the geographical isolates as an unresolved clade. Based on the available data it is concluded that the European isolates, formerly identified as Gyrodinium aureolum, Gyrodinium cf. aureolum, or Gymnodinium cf. nagasakiense, are conspecific with the Japanese Gymnodinium mikimotoi. An isolate from the Pettaquamscutt River, USA, is suggested to represent what Hulburt (1957) described as Gyrodinium aureolum. The LSU rDNA sequence data and ultrastructural characters in this isolate closely resemble those of Gymnodinium fuscum, the type species of Gymnodinium, and Gyrodinium aureolum Hulburt is therefore renamed Gymnodinium aureolum (Hulburt) G. Hansen, comb. nov.