Bacillus sphaericus (Bs) is a potential mosquito larvicide especially against Culex quinquefasciatus (Say), the vector of bancroftian filariasis. It is a gram-positive, aerobic and endospore-forming bacterium. During sporulation, it synthesizes binary endotoxins (molecular weight 42 and 51 kDa proteins) that are highly toxic to mosquito species. The mode of action of the binary toxin of this biolarvicide in the alimentary canal and the ultrastructural events in the tissues of the affected larvae have been demonstrated. Lysosomal components are the most important organelles involved in the metabolism of the foreign molecules encountered by the cells. In this paper, we report the ultrastructural changes in the midgut epithelial cells, with special emphasis on lysosomes (L), in untreated Cx. quinquefasciatus larvae and those treated with the Bs-IAB59 bacterial strain. In the Bs-treated larvae, the size of the L gradually increased, and within 16 h, fine filaments appeared and compartmentalized into small lamellar bodies, within the L. After 36 h, these lamellar bodies appeared to be collapsed, and later disintegrated in the 48th hour. In the untreated larvae, such ultrastructural changes in the L were not seen. These observations suggested that, though the target site of action of the Bs toxin is the midgut epithelial cells, ultrastructural changes in the L compartments play a vital role in the mortality of the mosquito larvae.