Crustacean aquaculture, and more specifically shrimp culture, faces several challenges in order to increase production yield while maintaining sustainability. The various disease outbreaks that have been continuously affecting the sector for almost two decades, together with the increasing demand for environmentally friendly aquaculture and the pressure from customers for safe and traceable products, are fundamentally modifying the culture practices of shrimp and other crustacean species. It is today well accepted that these challenges can only be faced through the development of better management practices together with technical innovations. Among the solutions currently considered, those relying on nutrition and intestinal health management can play a critical role. The application of probiotics in aquaculture has been developed in this context and is now widely applied in crustacean aquaculture as a complementary tool for management of disease. This development is mostly driven by practical and empirical approaches in shrimp farming; however, specific in-depth studies related to the biological effects and mechanisms of action of probiotics in crustaceans are gaining more importance. This chapter presents a review of the research conducted on probiotic applications in crustacean species with special emphasis on the modes of action investigated so far and the main benefits derived from it. The limits and future perspectives are also addressed.