In this study we investigated the Perkinsus genus for the SL RNA gene structure, intron prevalence, full-length mt cox1 and cytochrome b (cob) genes and their transcripts, and multiple-protein phylogenetic position. With the help of the GenBank database for six species and 33 unidentified Perkinsus sp. strains, and the P. marinus genome sequence, we performed thorough phylogenetic analyses and identification of introns in P. marinus. We paid special attention to histones because these proteins were thought to be absent in dinoflagellates until recently (for review see [21] ). We used deduced full-length amino acid (aa) sequences of 41 genes to reconstruct phylogenetic trees. Genomic structures and corresponding RNA sequences of the SL gene were analyzed. Sixtyeight Perkinsus full-length cDNAs obtained in our previous studies [8] , [14] were mapped to genome sequences to identify corresponding genes, and combined with 36 other reported genes to determine the frequency of introns. Although the Perkinsus clade shares commonalities with dinoflagellates, our data show that it is a unique lineage basal to the monophyletic clade of dinoflagellates.