The present paper describes a new species of Chloromyxum infecting the urinary bladder of the estuarine fish, Scatophagus argus, from the southwest coast of India. The parasite exhibited an overall prevalence of 41.93%; the prevalence is influenced by host size and seasons. Mature spores are subspherical, measure 9.40 ± 0.66 by 9.32 ± 0.87 μm, and are characterized by the presence of sutural and extra-sutural ridges, binucleated sporoplasm, and a pair of caudal extensions. Four pyriform, unequal polar capsules with raised polar filament discharge pores and ribbon-like polar filaments are present. Polar filament coils numbered four to five in large polar capsules and three in small polar capsules. Pansporoblast is irregular with granulated cytoplasm and has fine villosites on its surface. Plasmodia are spherical/irregular with monosporic and polysporic forms. In molecular and phylogenetic analysis, the myxosporean stands out with a high bootstrap value and was positioned as a sister branch of Chloromyxum kurisi. In view of the morphologic, morphometric, and molecular differences with the existing species of Chloromyxum, and considering the differences in hosts and geographic locations, the present species is treated as new and the name Chloromyxum argusi n. sp. is proposed.