BACKGROUND: The trunk canker caused by Botryosphaeria dothidea is a devastating disease for Chinese hickory (Carya cathayensis) in China. Chemical fungicides are commonly and repeatedly applied to control the disease; however, fungicide application raises major environmental and food safety issues. Ecofriendly biocontrol alternatives were urgently needed. Herein, the antifungal activity of a natural secondary metabolite, rapamycin, against B. dothidea and the effect of a rapamycin-producing Streptomyces hygroscopicus on C. cathayensis canker were investigated. RESULTS: The 50% effective concentrations (EC 50) of rapamycin against mycelial growth and spore germination on the potato dextrose agar were 5.1 × 10 −3 and 5.5× 10 −2 ∼g mL-1 , respectively, which were much lower than the EC 50 values of thiophanate-methyl. The hyphae of B. dothidea exhibited premature aging and wrinkling after treatment with rapamycin at 5.0 × 10 −3 ∼g mL-1. A rapamycin-producing bacterium S. hygroscopicus LYJ637 was batch produced and formulated in a carboxymethylcellulose/poly (vinyl alcohol) (CMC/PVA) blend and used for testing the efficiency of the bacterium in controlling Botryosphaeria canker in C. cathayensis. S. hygroscopicus exhibited high stability in the CMC/PVA blend. Results of a 3-year field experiment suggested that rapamycin formation reduced the occurrence of both developed cankers and new cankers, with an efficacy comparable to the treatment with thiophanate-methyl. CONCLUSION: The rapamycin-producing S. hygroscopicus LYJ637 carried in a CMC/PVA blend prevented effectively Botryosphaeria canker on Chinese hickory, which provides an alternative approach to chemical control strategies.