(Gaertn.) DC is a perennial plant belonging to the family Scropulariidae. The root of is used in oriental medicine and mainly grown using rootstock rather than seed cultivation, which gives rise to several problems including root rot, and results in a low productivity and poor quality. To solve the challenges involved in seed cultivation, our team previously used the formative features and genetic analysis of to determine the optimal in vitro tissue culture conditions for producing sterile culture seedlings and rootstocks of . The aim of the present study was to identify differences between standard rootstock seedlings (SR), culture rootstock seedlings (CR), and culture seedlings (CS) under field conditions. The reproductive characteristics of the aerial part were more robust while the area and length of leaves were smaller for SR than those for CR and CS. The characteristic that differed the most in SR was flowering, which did not occur in CR and CS. In addition, the fresh and dry weights of the subterranean parts of CR and CS were two-fold greater than those of SR. Fourier transform near-infrared (FT-NIR) analysis showed only slight differences between the chemical constituents of SR and its culture products, which was confirmed by measuring the content of catalpol, an indexing substance. Catalpol had a reduced content in the culture products compared to SR. However, this difference was not significant. Our findings will be useful for the identification of the best seedling type of to enable its mass production.