To understand the evolution of parasitism in the Alveolata, the phylogenetic relationship among the major lineages in this crown group must be resolved accurately. No consensus exists for the relationship between the Perkinsus genus with other alveolates, particularly the partition between apicomplexans and dinoflagellates. Taking advantage of SL RNA, mt gene characteristics, gene structure (e.g. intron density), and the increasing availability of functional protein sequences, robust evidence is provided in support of a relatively close relationship between Perkinsus spp. and dinoflagellates, in addition to a distinct non-dinoflagellate position of this alveolate pathogen.