The molecular basis of differential cultivar response to the induction of somatic embryogenesis was investigated by using the digoxigenin (DIG)-differential display with 2 eggplant (Solanum melongena L.) cultivars, Wase Shinkuro (WS) and Kumamoto Naga (KN). WS produced embryogenic callus (EC) which was capable of differentiating into mature somatic embryos while KN cultures treated similarly failed to differentiate somatic embryos. DIG-differential display of 0, 1, 2, 4, and 10-day old cultures of both cultivars revealed several PCR products derived from WS, but not from KN, at a crucial stage during embryogenesis. These results indicated that the cultivar difference in EC induction may be attributed, in part, to differences in mRNA expression between the cultivars during the culture process.