Ginsenosides of roots in Panax ginseng were analyzed by metabolic-targeting HPLC using the partial least squares discriminant analysis (PLS-DA) and compared depending on sowing methods between direct seeding and transplanting method. Score plots derived from PLS-DA could identify the sowing method between the direct seeding and transplanting method in P. ginseng roots. The ginsenoside compounds were assigned as Rg1, Re, Rf, Rg2, Rb1, Rc, Rb2, Rb3, and Rd. Contents of Re, Rf, Rg2, Rb1, Rc, Rb3, and Rd of main roots produced from the transplanting method were relatively higher than those of samples produced from direct seeding method. Also, contents of Rg1, Re, Rf, Rg2, Rb1, Rc, Rb2, Rb3, and Rd of lateral roots from the transplanted samples were relatively higher than those of samples produced from direct seeding method. Therefore, HPLC with PLS-DA analysis can be a straightforward tool for identification of ginsenosides in main or lateral roots of P. ginseng obtained from two different seeding methods between direct and transplanting methods.