Bombyx mori is an insect whose cocoon is used in the sericulture industry, which is an important activity in parts of southern Brazil. When parasitized by Bombyx mori nucleopolyhedrovirus (BmNPV) of the genus Alphabaculovirus (alphaBV), it develops nuclear polyhedrosis disease. In Brazil, an alphaBV was isolated from larvae of B. mori and various target tissues were identified. However, how this geographic viral isolate affects the rectum of silk moths was unknown. The rectum, a component of the cryptonephric system, acts to absorb water and mineral salts, and its importance for the metabolic balance of insects provoked interest in analyzing how it is affected by BmMNPV infection. Fifth instar B. mori larvae were inoculated with a viral suspension, and from the second to the ninth day post-inoculation, segments of the rectum (anterior and anal canal) were examined using light microscopy. The cryptonephric epithelial cells in the anterior region revealed no evidence of infection. However, from the fifth day post-inoculation, cells of the anal canal showed cytopathologies characteristic of alphaBV. Infection of the anal canal and other surrounding tissues led to tissue disorganization, with accumulation of polyhedra in the perinephric space and compartmentalization of the cryptonephric system, promoting changes in the fecal pellets, signalling physiological changes. These observations contribute to our understanding of the infectious cycle of BmMNPV in B. mori.