Nosema bombycis is a pathogen causing pebrine disease of the mulberry silkworm, Bombyx mori. The disease spreads mainly through transovarian transmission of environmental spore and secondarily through contaminated food, rearing appliances, etc. by primary spores. Ultra-structure studies using Scanning and Transmission Electron Microscopy of the two spores revealed differences in the primary spore which contained a Short Polar Tube (ST) with a thin wall (< 200 nm), and the environmental spore which contained a Long Polar Tube (LT) with a thick wall (> 200 nm). It is observed that the yield of spore with LT is highest in female moths, whereas, it is spores with ST are highest in male moths. Besides ultra-structures, the development pattern of the two types of spores is also different. It is an interesting finding in the present study that, spores of N. bombycis produced two types of spores and multiplied in different gender under the influence of the host’s reproductive role and physiology for transmission of disease. The detailed study on ultra-structure of disporous N. bombycis in both the sexes of B. mori along with their development in the life cycle stages of silkworms with special reference to the inoculum concentration of spore is discussed.