The morphology and genetic affinity of a novel raphidophyte belonging to the genus <i>Chattonella</i> Biecheler is described for the first time from the Oman Sea along the south-east coast of Iran. While morphologically very similar to <i>Chattonella subsalsa</i> Biecheler, the Iranian isolates contain a distinct red eyespot. A comparison of LSU-rDNA and rDNA-ITS show that the Iranian isolate is genetically distinct from other <i>Chattonella subsalsa</i> strains isolated from across a wide global range and indicates that the Iranian isolates represent a distinct species related to <i>Chattonella subsalsa</i>.