The Culex (Cx.) pipiens mosquito is the main vector of Filariasis and Rift Valley Fever in Egypt. Bacillus (B.) sphaericus is a mosquitocidal bacterium that was recently developed as a commercial larvicide and is used to control pestiferous and vector mosquitos worldwide. Whereas B. sphaericus is highly active against larvae of Culex.The 4^th larval instar of Cx. pipiens were dissected at 2, 10 and 14 hrs post-treatment with B. sphaericus, then the alimentary canal was fixed in 5% glutaraldehyde. Samples were dehydrated in an ethanol series, filtrated with epoxy resin, and stained with uranyl acetate. Semi-thin sections were stained with toluidine blue dye and then examined with 100X light microscopy (LM). The transverse sections (TS) of the mid and hindgut were examined by Transmission Electron Microscopes (TEM). The ultrastructural changes detected showed apoptosis, shrinkage, detachment from neighbours, nuclear degranulation, a number of vacuoles developed, and the bacteria began to penetrate the larval lumen. The damage to the midgut epithelium of the fourth larval instar of Cx. pipiens caused by B. sphaericus infection have an effect on the proliferation and differentiation of intestinal stem cells (ISC) in the midgut epithelium. It occurred simultaneously with a slight increase in cell division. Precursor stems cell proliferation and differentiation could replace the destroyed epithelial cells. The ISC regenerates the architecture of the midgut epithelium, thereby accelerating tissue repair. It was found that the number of stem cells and nuclei increase over time post-bacterial infection.