Abstract The facultative intracellular oyster parasite, Perkinsus marinus, taxonomically related to both dinoflagellates and apicomplexans, possesses at least two distinct genes ( PmSOD1 and PmSOD2) predicted to encode iron-containing superoxide dismutases (FeSOD). DNA blots and sequence analysis suggest that both PmSOD1 and PmSOD2 are single copy and are unlinked. PmSOD1 and PmSOD2 are composed of five and six exons, respectively. All introns are delimited by canonical GT/AG boundaries, and have some features more similar to apicomplexan than dinoflagellate introns. Interestingly, exon 1 of PmSOD2 encodes putative transmembrane and spacer domains with no homology to FeSODs, while exon 2 begins with a methionine codon and is homologous to the N-terminus of FeSODs. The position of introns is not highly conserved between PmSOD1 and PmSOD2, although one intron is in a similar location. Comparison of the intron positions of PmSOD1 and PmSOD2 to those of available apicomplexan FeSODs shows that the intron position shared by PmSOD1 and PmSOD2 is also observed in the FeSOD of Toxoplasma gondii. Comparison of the untranscribed regions 5′ and 3′ of the coding regions for PmSOD1 and PmSOD2 reveals few motifs in common. Instead, each gene possesses a distinct set of putative upstream transcription factor binding sites. Although the proteins encoded by PmSOD1 and PmSOD2 are only 38% identical to each other, homology modeling indicates that they have nearly identical active site structures. The divergent genomic organizations of two FeSOD genes in the same organism illustrates the complexity of the antioxidant system of even simple, early-branching protists such as P. marinus.