ABSTRACT-Recently, a microsporidian infection was found in the trunk muscle of hatchery-bred juvenile spotted halibut Verasper variegatus. The disease occurred from mid-July to the end of September 2007 and the cumulative mortality reached approximately 20%. Infected fish showed the external sign of a concave body surface on the eyed side, and the microsporidian parasite formed numerous 'cysts' in the muscle. These characteristics resembled 'beko' disease caused by Microsporidium seriolae from cultured yellowtail Seriola quinqueradiata, Microsporidium sp. from red sea bream Pagrus major (RSB) and Microsporidium sp. from gilthead sea bream Sparus aurata (GSB), but several differences were observed in associated pathological findings such as internal hemorrhage around the 'cysts'. Average dimensions of spores from spotted halibut (SH) were 3.07 × 2.13 µm, which were relatively smaller than those of M. seriolae, Microsporidium sp. RSB and Microsporidium sp. GSB, but the ranges of measurements overlapped among them. Molecular analysis of rDNA sequences suggested that the present parasite, provisionally named as Microsporidium sp. SH, was distinct from the other known species.