While observing silkworm larval samples received from field, microsporidian spores formed within the haemocytes of silkworm haemolymph were observed. The spores of microsporidian sp. were purified and characterized for morphological characters viz., size, shape as well as serological affinity with different Nosema spp. (M$_{11}$ and M$_{12}$). The infectivity of the isolated spores to silkworm was also studied. The microsporidian sp. was found to be highly pathogenic to silkworm, B. mori. The isolated microsporidian sp. was designated as NIK-5hm, which formed ovocylindrical spore in the haemocytes of silkworm and differed in spore size (length, 4.55 $mu$m & width, 2.10 $mu$m) and shape from Nosema bombycis (NIK-ls), NIK-2r (Nosema sp. Mysore [3.6 & 2.8 $mu$m]), NIK-3h (Nosema sp. M$_{11}$ [3.8 & 1.8 $mu$m]), NIK-4m (Nosema sp. M$_{12}$ [5.0 & 2.1 $mu$m]) and Lb$_{ms}$ (Nosema sp. in Lamerine breed of silkworm [4.36 & 2.14]). In immonological test (Latex agglutination test), the isolated microsporidian spores did not react with antibody sensitized latex particles of N. bombycis, M$_{11}$, M$_{12}$ and Lb$_{ms}$ and thus are different type of microsporidian sp., parasitic to silkworm, Bombyx mori L.