In the present study, Henneguya bicaudi n. sp. infecting gills of Cirrhinus mrigala (Ham.) an Indian major carp from Harike Wetland in Punjab, India, has been described on the basis of myxospore morphology and partial amplification of the SSU rRNA gene. The pseudocysts of H. bicaudi n. sp. were located within the gill filament, whitish with round to irregular outer margin and 0.5-0.7 mm in diameter, 3-4 pseudocysts each containing about 50-100 myxospores were detected per gill. Mature myxospores were oblongate, 21.0 × 6.2 μm had a caudal appendage bifurcating into two thin thread-like branches starting posterior to middle of its length. The two equal polar capsules were 3.14 × 2.02 μm. The present species was compared morphologically with 21 species of the genus Henneguya infecting fresh water fishes in India and related geographical area. H. bicaudi n. sp. differed in having a peculiar oblongate shape and size of the myxospore, equal polar capsules, and also by the location of the point of bifurcation of the caudal appendage. 18S rDNA sequences of H. bicaudi n. sp. obtained revealed 96% homogeneity with H. pseudorhinogobi (Kageyama et al., Fish Sci 75:657-663, 2009) infecting gill filaments of Rhinogobius sp. (Rutter, PANS Philad 56-90, 1897) in Japan. The intensity of infection was determined by the gill pseudocyst index (GPI) based on the number of countable pseudocysts by stereo zoom trinocular microscopy per gill (on one side).