How to keep the intestinal health of fishes in the intensive and high-density farming system is an important issue in aquaculture. In 1980s, probiotics were first used in fisheries. Application of probiotics has been regarded as an environment-friendly and effective strategy in aquaculture since then. At present, the commonly used probiotic microorganisms include Bacillus spp., Lactobacillus spp., Lactococcus spp. and Saccharomyces. Probiotics maintain the gut health of fish by inhibiting the proliferation of pathogenic microorganisms, improving the integrity of fish intestinal barriers, modulating the composition of intestinal microbiota and regulating the intestinal immune functions. However, more researches still need to be conducted to reveal the exact function of probiotics. Here, the application of probiotics and their possible mechanisms were summarized, and furthermore, the challenges and the future direction of probiotics in aquaculture were also discussed.