Bupleurum has been widely used for the treatment of chronic hepatitis and inflammatory diseases. The plant regulator methyl jasmonate (MeJA) mediates diverse developmental processes and defense responses. In this study, MeJA was applied to root suspension of Bupleurum kaoi for its ability to stimulate plant defenses and saponin production. Employing a cDNA microarray containing about 750 ESTs, generated with the PCR-Select cDNA Subtraction kit as probe sets, we profiled the transcriptome of MJ induction at different time intervals. The genes up regulated by MeJA treatment include those involved in jasmonate biosynthesis, secondary metabolism, cell-wall formation, and stress-protection and defenses. Transcript levels of the BkAS and Bkdef genes were enhanced by MeJA and affected by developmental stage but not by salicylic acid. The BkAS encodes -amyrin synthase which is a rate-limiting enzyme of saikosaponins biosynthesis. The BkDF1 and BkDF2 encode proteins belonging to group II of plant defensins. Expression of BkDF1 in root and leaves, and the antifungal activity against at least some tested pathogens indicated that BkDF1 may serve a role in protection of these organs against a range of pathogens.