ABSTRACT Vibrio cholerae is an estuarine bacterium and an intestinal pathogen of humans that causes severe epidemic diarrhea. In the absence of adequate mammalian models in which to study the interaction of V. cholerae with the host intestinal innate immune system, we have implemented Drosophila melanogaster as a surrogate host. We previously showed that immune deficiency pathway loss-of-function and mustard gain-of-function mutants are less susceptible to V. cholerae infection. We find that although the overall burden of intestinal bacteria is not significantly different from that of control flies, intestinal stem cell (ISC) division is increased in these mutants. This led us to examine the effect of V. cholerae on ISC division. We report that V. cholerae infection and cholera toxin decrease ISC division. Because IMD pathway and Mustard mutants, which are resistant to V. cholerae , maintain higher levels of ISC division during V. cholerae infection, we hypothesize that suppression of ISC division is a virulence strategy of V. cholerae and that accelerated epithelial regeneration protects the host against V. cholerae . Extension of these findings to mammals awaits the development of an adequate experimental model. IMPORTANCE Here we show that Vibrio cholerae and cholera toxin suppress intestinal stem cell (ISC) division. This is the first evidence of manipulation of ISC division by V. cholerae and demonstrates the utility of the Drosophila model in generating novel hypotheses regarding the interaction of V. cholerae with the intestinal epithelium. Furthermore, we add to the body of data suggesting that the IMD pathway and the Mustard protein modulate ISC division independently of the overall load of commensal intestinal bacteria.