Abstract: With the rapid development of aquaculture, the limit resulted from infective parasites is being significant. In a routine investigation of ocean fishery, a new species of fish parasitic microsporidium was found in the abdominal cavity of Epinephelus akaara at Daya Wan in South China Sea in October, 2001. To our best knowledge this is the first report of parasitic microsporidium in groupers in the world. The type specimens were preserved in the South China Sea Institute of Oceanology, Chinese Academy of Sciences.Through routine taxonomic detection, we placed it in the genus of Glugea, and named it Glugea epinephelus sp nov for it owns the obvious and representative characteristics of Glugea genus. However, the specie reported in the present study have significant differences compared to other microsporidiums belong to Glugea genus reported until now. Among the differences, it is most significant that the xenomas of Glugea epinephelus are black. For more validating the taxonomic position of the microsporidium, the SSUrRNA sequence of the pathogen was amplified using a specific pair primer. We compared the SSUrRNA sequences of Glugea epinephelus and that of other 15 species from GeneBank. The constructed homology tree and phylogenetic tree of these species displayed that there are highest homology between Glugea epinephelus and G. anomala, the type specie of Glugea genus, but exist relative significant genetic differences with Pleistophora typicalis, the type specie of Pleistophora genus and Loma salmonae, the type specie of Loma genus. As a result, we thought that the microsporidium was a new specie and belong to Glugea genus.