Abstract Under the Stand-based Silvicultural Management System, conifer seedlings are planted in natural forests to assist natural regeneration. For this purpose, seedlings of Abies sachalinensis, Picea jezoensis, and Picea glehnii, which are major species of natural forest, are raised in a nursery at the University of Tokyo Hokkaido Forest (UTHF). Clonal seed orchards have been established as seed sources for A. sachalinensis and P. jezoensis, while seed stands are designated in natural forests for P. glehnii. To minimize genetic disturbance and maintain genetic diversity, ortets of seed trees that constitute the seed orchards were selected from natural forests within the UTHF. The seedlings are outplanted after a raising period of 6–7 years. Most of the raised seedlings are bare-rooted, while containerized seedlings are currently under trial. During the raising period, some diseases, such as Racodium snow blight and damping-off, threaten seedling production. These diseases are managed through cultural and chemical control methods. Care should also be taken to mitigate damage caused by extreme climatic events such as late frost, heat waves, and drought under ongoing climate change.