The present study describes a new species of myxosporean, Sphaeromyxa cornuti n. sp. infecting the gallbladder of the Moorish idol, Zanclus cornutus (Linnaeus 1758) collected from Lakshadweep waters of the Arabian Sea. Fish were collected using traps and cages. The morphology of mature spores recovered from the gallbladder of Z. cornutus was studied under Nomarski Differential Interference Contrast (DIC) optics. The molecular and phylogenetic analyses were based on SSU rDNA. Sphaeromyxa cornuti n. sp. is characterized by arcuate myxospores with tapering extremities and round ends in valvular, and slightly sigmoid in sutural views (19.2-24.7 µm × 4.1-5.7µm). The two polar capsules are unequally elongate-ovoid in shape and positioned at opposite ends of the spore (6.2-9.7µm × 1.7-2.6µm). Each encloses an irregularly folded, ribbon-like polar tubule, which is oriented parallel to polar capsule axis. In molecular and phylogenetic analyses, the present myxosporean revealed significant differences with related forms and clustered together with S. hellandi within the 'incurvata' group of the Sphaeromyxa clade with high nodal support. Morphological, morphometric, molecular and phylogenetic differences between our material and previously described species of Sphaeromyxa, along with host and geographic variations indicate that the present myxosporean is unique and the name Sphaeromyxa cornuti n. sp. is proposed. This forms the first report of a myxosporean parasite-infecting Z. cornutus.