Two novel species of Ceratomyxa infecting marine ornamental fishes from Indian waters are described. Marine ornamentals, Chaetodon collare and Chaetodon decussatus, collected from Vizhinjam, along the southwest coast of India and Acanthurus leucosternon collected from Lakshadweep islands ofArabian Sea revealed Ceratomyxa infections in their gall bladders. Mature spores of Ceratomyxa from Chaetodon collare and Chaetodon decussatus were elongate and slightly crescentic, with rounded ends, and measured 5.20± 0.32 μm in length and 16.32 ± 1.29 μm in thickness. Polar capsules spherical, equal in size and measured 2.23 ± 0.16 μm long and 2.24± 0.20 μm wide. Posterior angle measured 157.75 ± 8.650. Principle Component Analysis and molecular analysis using partial SSUrDNA sequences showed the isolates from these two hosts to be identical. Morphological, morphometric and molecular analysis using partial SSUrDNA sequences revealed the taxonomic novelty of isolates and are hence treated as Ceratomyxa collarae n. sp. Mature spores of Ceratomyxa from Acanthurus leucosternon were elongate, slightly tapering with rounded ends, and measured 7.34 ±0.92 μm in length and 24.37 ± 2.34 μm in thickness. Shell valves were equal, joined by a narrow suture line. Polar capsules spherical in shape, equal in size, 2.59±0.32 μm long and 2.46 ± 0.32 μm wide, and polar filament measured 18.68 ±2.54 μm. Based on morphological, morphometric and molecular analyses, the present species of Ceratomyxa is distinct, considered as a new species and named Ceratomyxa leucosternoni n. sp. The paper also discusses the prevalence of the recovered parasites and host specificity of Ceratomyxa collarae n. sp.