Ultrastructure of Gut of Silkworm, Bombyx mori L. infected with newly isolated microsporidian NIK-5hm shows hypertrophy and structural disorganization in the infected tissue. From 0 to 6 DPI, there were no clear histopathological symptoms. On 8 DPI, histo-pathological symptoms were initiated and few midgut goblet and columnar cells developed abnormality and became shrunken. On 10 DPI, The cells were less stained throughout the progressive infection. On 12 DPI multi-layered and undifferentiated regenerative nidi cells were found. The infected cells were continuously pushed off into the midgut lumen due to newly developed immature cells of regenerative nidi cells. The number of regenerative nidi cells were more in this tolerant breed (PM) compared to susceptible breed (CSR2). From 12 DPI, the damaged goblet cells were continuously replaced by the newly formed regenerative nidi cells.