Experiments were conducted with the aim to compare the agronomic characteristics of two new wasabi lines, i.e. 79-S-1 and 79-I- with three cultured varieties, i.e. Tainung NO. 1,70-I-1 and Local cultivar. Electrophoresis methods of soluble protein and peroxidase were used for varietal identification. Experimental data showed that the aboveground weight of the two tested lines was higher than that of three check varieties. However, no significant difference was found in rhizome yield per plant among them. Electrophoresis analysis indicated that peroxidase, rather than soluble protein, may be used as an indicator to verify difference among these wasabi lines/varieties.