The gene ap36 encoding a protein elicitor from Alternaria sp. was fused downstream of the slh (S-layer homology) motif of Bacillus thuringiensis S-layer protein gene ctc. The recombinant gene was then transferred into B. thuringiensis plasmid-free derivative strain BMB171. Sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE) showed that the SLH–Ap36 fusion protein was expressed in B. thuringiensis BMB171. After tomato (Lycopersicum esculentum) leaves were treated for 90 min with the recombinant strain cultured at 28°C for 24 h, the activity of peroxidase and the amount of proline of tomato leaves were increased to 57.14% and 131.59%, respectively, compared to the control, and after the tomato leaves were treated with the cultured recombinant strain for 4 days, the activity of phenylalanine ammonia lyase was also higher than that in the control. Furthermore, tubers of treated potato (Solanum tuberosum) plants showed higher resistance to rot disease caused by Erwinia corotovora SCG1 compared to the control treatments.