Thalassochytrium gracilariopsidis gen. et sp. nov. is an endosymbiotic, polycentric, zoosporic fungus that infected cultures of the red alga Gracilariopsis sp. Based on the posteriorly uniflagellate zoospore and the platelike cristae of the mitochondria, the fungus is placed in the Chytridiomycota. Ultrastructurally, the fungal zoospore is distinguished by the anterior position of the kinetosome, a unique microbody‐lipid globule complex, an electron‐opaque helix associated with the kinetosome and lipid globules, and a beaked nucleus. Zoospores are positively phototactic, and the unusual helix might constitute part of the photosensory apparatus. Zoospores lack certain taxonomically important structures, such as a rumposome, props, a nonflagellated kinetosome, and flagellar roots. The organism does not fit into any described genus, and the features of its zoospore differ from those of any described order. The fungal thallus is polycentric with multinucleate, septate hyphae. Haustoria form within the algal cells. The fungus does not appear to cause major harm to its host and seems to be host specific. However, during intense sporulation of the fungus, degradation of host chloroplasts was observed in medullary cells.