Jerusalem artichoke (Helianthus tuberosus L.) is a multipurpose crop grown for bio-fuel, feed additive and functional food products. Stem rot disease caused by Sclerotium rolfsii Sacc. is an important threat for Jerusalem artichoke production in the tropics, and disease control using induced resistance strategy is worth exploring. The objective of this study were to investigate the induction of chitinase and b-1,3-glucanase activities in leaves of H. tuberosus after treated with microorganisms, Bacillus firmus BSR 032, Trichoderma harzianum T9 and mycorrhizal fungus, Glomus clarum and to evaluate their efficacy on controlling the disease under green house condition. Increase in chitinase and b-1,3-glucanase activity and reduction in disease incidence were observed for the plants treated with these antagonistic microorganisms. The highest and most consistent increase in chitinase and b-1,3-glucanase was observed in the plants treated with T. harzianum T9 followed by T. harzianum T9+G. clarum, and b-1,3-glucanase was found at higher activity than chitinase. The T. harzianum T9 could reduced the disease incidence of 44.4%, followed by T. harzianum T9+G. clarum (22.8%), B. firmus BSR 032+G. clarum (15%), B. firmus BSR032 (8.6%) and G. clarum (4.2%), respectively. This T. harzianum T9 is a promising antagonistic microorganism for controlling stem rot disease.