The vacuolar ATPase (V-ATPase) is a multifunctional enzyme that consists of several subunits. Subunit B is a part of the catalytic domain of the enzyme. The result of the RT-PCR suggested that the V-ATPase B subunit is a ubiquitous gene. 24 h after the larvae were infected with the Bombyx mori nucleopolyhedrovirus (BmNPV), the expression level of the V-ATPase B subunit in the midgut of the resistant strain NB was about 3 times higher than in the susceptible strain 306, and then the expression level of the V-ATPase B subunit decreased rapidly to a very low level. This indicated that the virus may cause a lot of changes of physiological conditions in the midgut. Localization of the V-ATPase B subunit was attempted in midgut cells of Bombyx mori by immunohistochemistry. The immunohistochemical localization with the antibody against the B subunit revealed a positive staining in goblet cell apical membranes of Bombyx mori midgut cells as well as in the midgut of Manduca sexta. This sequence has been registered in GenBank under the accession number EU727173.