The present study illustrates the transformation ability of two wild-type bacterial strains of Rhizobium rhizogenes (MTCC 532 and MTCC 2364) on the embryogenic callus and callus-derived plantlets of a threatened Indian orchid, Dendrobium ovatum. Co-culture of the bacterium with the explants gave marginal hairy root phenotype that failed to multiply in the culture medium. Some primary and secondary metabolites were subdued in infected explants. Moscatilin, the stilbenoid active principle in D. ovatum, was found below the detection limit. The presence of two metabolites viz., Laudanosine, a benzyltetrahydroisoquinoline alkaloid and Lyciumin B, a cyclic peptide, were detected exclusively in the infected explants. The subjugated amino acids and phenolics in the infected plantlets were routed to produce phytoanticipins, and phenanthrenes, strengthening the defence mechanism in infected tissues. This research implies that the plant's defence mechanism activation could have prevented the extensive hairy root formation in the explants, even though nodulations and phenotype transitions were witnessed. Moscatilin has a structural resemblance with Resveratrol, a phytoalexin that combats bacterial and fungal pathogens. The study favours the possibility of Moscatlin being a precursor for phenanthrene compounds, thereby serving as a 'phytoanticipin' during the infection phase.