It is a difficult question. Japan is filled with beautiful mountains and hiking trails. I am not really a hiker but to name few, I'd say:
Located in Hokkaido Prefecture and one of the World Heritage Sites. The hiking trail includes five beautiful lakes, full of nature and wild animals. Wild Ezo-deer comes surprisingly close to you!
- Yakushima Island
Another World Heritage Site but located in Kagoshima Prefecture. The island can be reached by airplane or ferry from Kagoshima. Yakushima Island has a total different natural systems and it is fun to experience both Shiretoko and Yakushima to feel the range of nature in Japan.
Yakusugi, the unique kind of cedar is famous here and people start hiking from 5:00 am to see Jomonsugi, the huge Yakusugi tree said to be more than 1,000 years old.
- Mt. Fuji
Climbing Mt. Fuji is a must-have experience if you are interested in hiking. The highest mountain in Japan will sure give you an unforgettable views.
These articles may help you planning: