Mosquitoes have a diverse intestinal microbiota which plays essential roles in a variety of the insect's physiological functions. This microbiota can also influence vector competence for human pathogens in multiple ways, including immune system activation or suppression, the regulation of other physiological processes, direct inhibition of the pathogen, and competition with the pathogen for limited resources. The mosquito's intestinal microbiome is responsible for eliciting basal immune activity, which in addition to preventing overproliferation of bacteria, also acts against exogenous bacteria, fungi, parasites, and viruses. Some endogenous microorganisms directly impair pathogen infectivity or viability, independent of the mosquito, through mechanisms involving reactive oxygen species and other more stable bacteria-/fungi-produced metabolites. Other microorganisms, particularly those with entomopathogenic activity, can influence pathogen transmission by shaping mosquito population dynamics. Exploration of the mosquito gut microbiome's antipathogen and entomopathogenic activities can provide essential knowledge for the development of novel disease-control approaches based on blocking pathogen infection in the mosquito and vertebrate host and/or shortening the mosquito's lifespan.