In the cytochrome c oxidase subunit I (cox1) gene of four raphidophycean flagellates Chattonella antiqua, C. marina, C. ovata, and C. minima we found two group II introns described here as Chattonella cox1-i1 and Chattonella cox1-i2 encoding an open reading frame (ORF) comprised of three domains: reverse transcriptase (RT), RNA maturase (Ma) and zinc finger (H-N-H) endonuclease domains. The secondary structures show both Chattonella cox1-i1 and Chattonella cox1-i2 belong to group IIA1, albeit the former possesses a group IIB- like secondary structural character in the epsilon' region of arm I. Our phylogenetic analysis inferred from RT domain sequences of the intronic ORF, comparison of the insertionsites, and the secondary structures of the introns suggests that Chattonella cox1-i1 likely shares an evolutionary origin with the group II introns inserted in cox1 genes of five phylogenetically diverged eukaryotes. In contrast, Chattonella cox1-i2 was suggested to bear a close evolutionary affinity to the group II introns found in diatom cox 1 genes. The RT domain-based phylogeny shows a tree topology in which Chattonella cox1-i2 is nested in the diatom sequences suggesting that a diatom-to-Chattonella intron transfer has taken place. Finally, we found no intron in cox1 genes from deeper-branching raphidophyceans. Based on parsimonious discussion, Chattonella cox1-i1 and Chattonellacox1-i2 have invaded into the cox1 gene of an ancestral Chattonella cellafter diverging from C. subsalsa. (C) 2009 Elsevier GmbH. All rights reserved.