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Gensokyo, the area encompassed by the Hakurei Border, is a landlocked territory at least some tens of kilometers in diameter, although its exact size has not been mentioned in canon materials. Notable geographic features include the Youkai Mountain with communities of kappa at its base, tengu at its peak, and the Moriya Shrine at a lake near the top; the Forest of Magic; the Bamboo Forest of the Lost where Eientei is located; the Misty Lake surrounding the Scarlet Devil Mansion; the Human Village, which is assumed to be in a fertile valley; and the Sanzu River separating Gensokyo from Higan.

Although passing through the Hakurei Border to the outside world is virtually impossible for anyone besides Yukari Yakumo, it is significantly easier for Gensokyo denizens to access domains of gods, demons, and dead souls which are not strictly part of Gensokyo itself. These include Higan, the Netherworld, Makai, the Celestial realm seen in Scarlet Weather Rhapsody, and the underground abandoned Hell where Subterranean Animism is set.

Cage in Lunatic Runagate Chapter 4 reveals that the Youkai Mountain preserves the original appearance of Mount Yatsugatake before Sakuya-hime, the goddess of Mount Fuji, tore it down out of jealousy. In the outside world today, the remnants of the mountain can be seen as the Yatsugatake mountain range in Yatsugatake-Chūshin Kōgen Quasi-National Park between Nagano and Yamanashi Prefectures, providing an indication of where Gensokyo would be located in Japan. Lake Suwa (諏訪湖, Suwa-ko), which Suwako Moriya was named after, is located nearby.