Nosema ceranaeis an intracellular parasite invading the midgut of honeybees, which causes serious nosemosis implicated in honeybee colony losses worldwide. The core gut microbiota is involved in protecting against parasitism, and the genetically engineering of the native gut symbionts provides a novel and efficient way to fight pathogens. Here, using laboratory-generated bees mono-associated with gut members, we find thatSnodgrassella alviinhibit microsporidia proliferation, potentially via the stimulation of host oxidant-mediated immune response. Accordingly,N. ceranaeemploys the thioredoxin and glutathione systems to defend against oxidative stress and maintain a balanced redox equilibrium, which is essential for the infection process. We knock down the gene expression using nanoparticle-mediated RNA interference, which targets the γ-glutamyl-cysteine synthetase and thioredoxin reductase genes of microsporidia. It significantly reduces the spore load, confirming the importance of the antioxidant mechanism for the intracellular invasion of theN. ceranaeparasite. Finally, we genetically modify the symbioticS. alvito deliver dsRNA corresponding to the genes involved in the redox system of the microsporidia. The engineeredS. alviinduces RNA interference and represses parasite gene expression, thereby inhibits the parasitism significantly. Specifically,N. ceranaeis most suppressed by the recombinant strain corresponding to the glutathione synthetase or by a mixture of bacteria expressing variable dsRNA. Our findings extend our previous understanding of the protection of gut symbionts againstN. ceranaeand provide a symbiont-mediated RNAi system for inhibiting microsporidia infection in honeybees.