Oodinium pouchetii (Lemmermann, 1899) Chatton, 1912, the first described parasitic dinoflagellate, is the type of the Oodiniaceae Chatton, 1920. In the taxonomical schemes, this family of metazoan parasites includes Amyloodinium Brown & Hovasse, 1946 and Piscinoodinium Lom, 1981 that are responsible of important damages in fish aquaculture. Species of Oodinium Chatton, 1912 have unique characteristics such as the possession of both non-dinokaryotic and dinokaryotic nuclei within the life-cycle, and the absence of the transversal (cingulum) and longitudinal (sulcus) surface grooves in the parasitic stage. We provide the first molecular data for the genus Oodinium from specimens of O. pouchetii infecting the chordate Oikopleura sp. (Tunicata: Appendicularia) off the coasts of Brazil. Although O. pouchetii lacks dinokaryotic characters in the parasitic stage, the SSU rDNA phylogeny revealed that it forms a distinct fast-evolved clade that branches among the dinokaryotic dinoflagellates. However, there is no clear relationship with other dinoflagellates. Hence, the taxonomic affinity of the family Oodiniaceae is unclear at the moment.