- Yaeyama Islands, Ryukyu Islands, Okinawa Prefecture6 objects
- Yama District, Fukushima Prefecture, South Tohoku3 objects
- Yamagata (historical village), Kuji, Iwate Prefecture1 objects
- Yamagata Prefecture, South Tohoku, Tohoku region14 objects
- Yodogawa (Yodokawa), Tsuruoka, Yamagata Prefecture1 objects
- Yonezawa, Yamagata Prefecture, South Tohoku2 objects
- Yosemite National Park, California1 objects
- Yuda (historical town), Waga District, Iwate Prefecture3 objects
- Yunishikawa, NikkÅ, Tochigi Prefecture7 objects
- Yunotani village (historical), Kitauonuma District (historical), Niigata Prefecture1 objects