The phylogenetic affinities of the oyster pathogen Perkinsus marinus w
ere investigated with morphology, 18S-like rDNA data and actin sequenc
e data. Morphological investigations revealed that Perkinsus species d
o not have a conoid and that other criteria which have been used to pl
ace them in the Apicomplexa are general to alveolates. When considered
separately, 18S-like rDNA and actin data sets each support a closer a
ffinity for Perkinsus marinus with the dinoflagellates. However, each
of these separate analyses possess their own biases and weaknesses. Us
e of the phylogenetic principle of 'total evidence' in which data sets
are combined in simultaneous analysis yielded a more robust hypothesi
s that is stable both to character and taxonomic sampling. The resulti
ng cladogram strongly corroborates the placement of Perkinsus species
with the Dinoflagellida and not with the Apicomplexa.