Abstract Aquaculture is a fast‐growing and rapidly expanding industry in the world. Probiotics are widely used in aquaculture and have provided benefits to aquatic animal health, and it is also a promising alternative to antibiotics for control of fish diseases. With the development of biotechnology, new expression systems and novel techniques for the surface display of heterologous proteins in surface of probiotics cells have been developed. This review provides an overview of the systems and strategies for displaying functional proteins on the surface of probiotics commonly used in aquaculture, which are Bacillus subtilis , Bacillus thuringiensis , lactic acid bacteria represented by Lactococcus lactis and yeast. Their applications in aquaculture especially for oral vaccine development afforded by this technology and prospects and challenges associated with this technology are also highlighted.