Benefits of seed priming in seedling establishment and tolerance to subsequent stress exposure are well reported. However, the molecular mechanisms underlying the priming mediated benefits are not much discovered. Results of our earlier experiments established that thiourea (TU) seed priming imparts cold tolerance to capsicum seedlings. Therefore, to understand molecular mechanisms underlying priming mediated cold stress tolerance, quantitative transcript expression of stress responsive genes involved in transcript regulation (CaCBF1A, CaCBF1B, Zinc Finger protein, CaWRKY30), osmotic adjustment (PROX1, P5CS, Osmotin), antioxidant defence (CAT2, APX, GST, GR1, Cu/Zn SOD, Mn SOD, Fe SOD), signaling (Annexin), movement of solutes and water (CaPIP1), and metabolite biosynthesis through phenylpropanoid pathway (CAH) was studied in response to cold (4 °C; 4 and 24 h) stress in seedlings grown from the TU primed, hydroprimed and unsoaked seeds. The transcript expression of CaWRKY30, PROX1, Osmotin, Cu/Zn SOD and CAH genes was either higher or induced earlier on cold exposure in thiourea priming than that of hydroprimed and unsoaked over the respective unstressed controls. The results thus suggest that the TU priming modulate expression of these genes thereby imparting cold tolerance in capsicum seedlings.