During the past two decades, the use of probiotics as an alternative to the use of antibiotics has shown to be promising in aquaculture, particularly in fish and shellfish larviculture. This article reviews the studies on probiotics in larviculture, focusing on the current knowledge of their in vivo mechanisms of action. The article highlights that the in vivo mechanisms of action largely remain to be unravelled. Several methodologies are suggested for further in vivo research, including studies on gut microbiota composition, the use of gnotobiotic animals as test models, and the application of molecular techniques to study host-microbe and microbe-microbe interactions.