Bacillus subtilis E20, an isolate from natto – a Japanese fermented soy product – is used in a wide variety of marine and freshwater aquatic species to enhance growth and immunity. This paper describes the cloning, expression and characterization of xylanase isolated from B. subtilis E20 in B. subtilis RIK1285. The BsXynE20 gene was identified to encode a 213‐amino‐acid protein for a glycoside hydrolase family 11 xylanase containing a 28‐residue signal peptide whose cleavage yields a 185‐residue mature protein with a predicted molecular weight of 20.25 kDa. The full length of the BsXynE20 gene was subcloned into the pBE‐S expression vector for secretory production of recombinant BsXynE20 in B. subtilis RIK1285. Western blot and zymogram analysis, respectively, revealed that recombinant BsXynE20 can be secreted into culture medium and is a functional xylanase. The xylanase exhibited optimal activity at pH 5.0–6.0 and 60°C. Using recombinant BsXynE20‐pretreated duckweed meal for feed preparation improved the growth performance of tilapia. Finally, we achieved secretive expression of functional BsXynE20, which can improve the nutrient utilization of a plant‐derived diet. Thus, the use of BsXynE20 may be beneficial for tilapia aquaculture.