Morphological features are the predominant criteria used to define species of marine dinoflagellates. Taxonomic problems with some toxic groups has led to the implementation of molecular taxonomy techniques and development of a genospecies concept. As a result, the relationships between “morphospecies” and “genospecies” has been questioned. In this study, the genetic differentiation between two sets of closely related morphospecies, Gymnodinium catenatum Graham/Gyrodinium impudicum Fraga and Alexandrium minutum Halim/Alexandrium lusitanicum Balech, were analyzed. The extent of morphological differentiation existing within these two groups is of the same order of magnitude. Analysis of cell surface antigens detected by preadsorbed serum, cell surface glycan moieties detected by lectins and sequencing of the D9 and D10 domains of the Large-subunit ribosomal RNA gene, showed that the extent of genetic differentiation existing between the dinofagellates Gymnodinium catenatum/Gyrodinium impudicum is substantial. Therefore, both morphological and genetic criteria resolve these organisms as two distinct entities. In contrast, Alexandrium minutum/Alexandrium lusitanicum were indistinguishable using the some suite of molecular markers. The findings demonstrated that classifications based on morphological criteria may be incongruous. On a practical level, molecular taxonomy provides useful tools to distinguish between morphologically similar microalgal species and furthermore can prevent misidentification of species such as Gymnodinium catenatum/Gyrodinium impudicum, a frequent occurrence when samples are fixed with Lugol's or formaldehyde solution.