This study provides morphological and molecular data of a new myxozoan species belonging to genus Myxobolus from the gill filaments of an endemic cyprinid fish from River Poonch in North West Himalaya, India. Parasitological observations under stereozoom binocular microscope revealed single large type of plasmodia 2–10 mm in diameter residing on the gill filament, while clinical signs revealed mucous laden gills. Infection was found in the 21 of 80 examined Schizothorax richardsonii with a prevelance of (26.25%). Mature spores appeared oval to spherical in frontal view, and broadly rounded posterior end measuring 8.56–10.02 (9.64) x 6.07–8.10 (7.06) μm. Two equal polar capsules were pyriform measuring 4.89 x 2.70 μm, and polar filaments coiled 5–6 turns. Phylogenetic analysis indicated that the obtained 18S rDNA sequence of M. himalayaensis sp. nov. (MK087655) did not match any available myxozoan sequence and was sister species to Henneguya doneci infecting gills of gibel carp Carassius gibelio from China and showing less than 95% sequence similarity with Myxobolus linzhiensis using BLAST search. Histological observations of infected gills revealed plasmodia of type FV 2 intrafilamental vascular type causing hypertrophy, hyperplasia, uplifting of epithelial cells and necrosis. © 2019