The phylogenetic position of a species of the free-living protist genus Colpodella is assessed using its SSU rDNA gene sequence in the context of a wide array of other alveolate taxa. Phylogenetic analyses indicates that this species is not related to species of Bodo as has previously been suggested. However, SSU rDNA data alone are insufficient to provide a wholly stable hypothesis of relationships for Colpodella sp. among the various alveolate phyla. Much of this instability can be attributed to alignment procedure sensitivity. Analyses of SSU rDNA and actin gene sequences in combination provide strong support for a species of Colpodella as sister group to the ciliates, irrespective of alignment procedure. Moreover, use of SSU rDNA data alone strongly support a recent common ancestry of the genera Perkinsus and Parvilucifera with the dinoflagellates, and not with the apicomplexans. These findings, and the nearly identical ultrastructural characteristics of Colpodella, Perkinsus, and Parvilucifera species, suggest that this morphology is the ancestral condition for all of Alveolata.