Tylophora indica, an indigenous medicinal plant, was transformed with the cryptogein gene to determine the effect of crypt gene on secondary metabolites in co-transformed roots and plants via Agrobacterium rhizogenes mediated transformation. The Ri crypt co-transformed roots and plants showed expression of crypt gene. Southern hybridization specifies that crypt gene has been transferred and positively integrated into the Ri crypt co-transformed plant. AFLP fingerprinting revealed high degree of genetic similarity among the Ri-transformed and Ri crypt co-transformed cultures. The expression of crypt gene stimulated phenolic compound accumulation in transformed root and plants while tylophorine content was comparable in Ri transformed and Ri crypt co-transformed root lines and plants. The Ri crypt co-transformed root lines showed significantly higher (p ≤ 0.05) phenolics production (caffeic acid, 1.8–2.9-fold; p-coumaric acid, 1.9-fold and ferulic acid, 1.5–2-fold) compared to Ri-transformed root lines. The roots of Ri crypt co-transformed plants showed a significantly (p ≤ 0.05) higher content of caffeic acid (1.19-fold) and ferulic acid (1.53-fold) than Ri-transformed plants. It is suggested that crypt-transformed plants can also be used as a tool to elucidate the biochemical basis of defense responses as phenolics are known to play a role in providing defense barriers to infection by pathogen. © 2016, Franciszek Górski Institute of Plant Physiology, Polish Academy of Sciences, Kraków.