The dinoflagellate Haidadinium ichthyophilum Buckland-Nicks, Reimchen and Garbary 1997 is an ectoparasite of Pacific herring (Clupea pallasii), causing serious skin lesions and mass mortalities. Its phylogenetic position within the dinoflagellates has been controversial. We sequenced the nuclear SSU and LSU ribosomal RNA genes of H. ichthyophilum and performed comprehensive phylogenetic analyses. Our results place H. ichthyophilum as an early-branching dinoflagellate.