The phylogenetic affinities of the oyster pathogen Perkinsus marinus were investigated with morphology, 18S-like rDNA data and actin sequence data. Morphological investigations revealed that Perkinsus species do not have a conoid and that other criteria which have been used to place them in the Apicomplexa are general to alveolates. When considered separately, 18S-like rDNA and actin data sets each support a closer affinity for Perkinsus marinus with the dinoflagellates. However, each of these separate analyses possess their own biases and weaknesses. Use of the phylogenetic principle of ‘total evidence’ in which data sets are combined in simultaneous analysis yielded a more robust hypothesis that is stable both to character and taxonomic sampling. The resulting cladogram strongly corroborates the placement of Perkinsus species with the Dinoflagellida and not with the Apicomplexa.