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This category contains articles related to the native flora of Japan. Taxa of the lowest rank are always included. Higher taxa are included only if endemic. Japan is within the larger region of East Asia.

For the purposes of this category, "Japan" is defined in accordance with the World Geographical Scheme for Recording Plant Distributions. That is, the geographic region is defined as including the following areas, typically defined by the political boundaries of its constituents:

Includes

• Hokkaido (includes: Okushiri Island, Rebun Island, Rishiri Island)
• Honshu (includes: Aogashima, Awaji Island, the Oki Islands, Hachijō-jima, Heigun-tō of the Bōyo Islands, Ieshima, Inamba-jima, Innoshima, Izu Islands, Kōzu-shima, Kurahashi, Liancourt Rocks, Lot's Wife, Mikura-jima, Miyake-jima, Myojin-jima, Naga-shima, Nii-jima, Sado Island, Shikine-jima, Smith Island (Japan), Ya-shima, Yashiro island)
• Kyushu (includes: Fukue Island and other Gotō Islands, Himeshima, Iki Island, Koshikijima Islands, Ōsumi Islands, Tsushima Island)
• Shikoku (includes: Hakata-shima, Nako-jima, Omi-shoto, Shōdo Island, Teshima, Uoshima)

Excludes

• Volcano Islands (Kazan-retto) in East Asia
• Minami-Tori-shima (Marcus Island) in the Northwestern Pacific
• Ryukyu Islands, and Bonin Islands (Ogasawara-shoto) in East Asia