This was for us a two months journey, we ride it all at a slow pace. It can be done way faster with any other kind of transportation.
Links in the articles bring you to the full travel journal article about each destination, unfortunately those are still only in Italian so use your translator.
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Below is the complete map of our bicycle trip in Japan. It's the complete GPS recording of the journey.
Click on the track to get the elevation profile, you can also use the search tool to find a specific location and display the GPX track of reference.
From Fukuoka harbour (coming by ferry from Busan, South Korea), we went down to Kumamoto crossing a small range of lush green hills, then to Amakusa islands, a spectacular archipelago in the Ariake Sea (the big gulf of western Kyushu), mostly connected by bridges. Stunning views, quiet roads and some nice beach with cristal clear water.
From there we dropped by ferry on the island of Nagashima (ferry route Ushibuka - Kuranomoto, 750Yen, 30min) another beautiful island with stunning beaches and many weird statues of Shinto gods, then we followed the spectacular coast and cut along a river to Kagoshima and it's nervous volcano
Going to Taketa visit the inspiring shrine, it's a thousand tori shrine dedicated to the Inari (foxes god), look for the huge tori in the centre of town and follow them.
From here the ride to Oita it's a flat good coastline until the city and the ferry jetty a little further. Here runs the cheapest ferry to Shikoku (to Misaki jetty in the Sadamisaki peninsula, can't remember the price, not so cheap anyway)
This big loop of Kyushu took us almost one month, we went very slow (avg 50km per day) but never been two nights in the same place.
From the narrow Sadamisaki peninsula, with it's fruit tree terrace on the steep slopes and the quiet fishermen villages, the ride along the coast to the castle town of Matsuyama it's scenic.
From here we took the famous Shiminami Kaido, the 70km cycling path above the islands of the Seto Inland Sea.
The path it's very popular to local cyclists and is spectaculars on some parts. But you will end up in a very busy area of Honshu (the biggest of the Japanese four major islands) and we regret that. I would suggest to ride more of Shikoku instead and take a ferry later (the biggest suspended bridge in the world connects eastern Shikoku with Honshu in Kobe, thought i think it's not possible to bike it).
In Osaka there's a free camping spot in the Tsurumi Ryokuchi park (GPS coordinates: N 34° 43' 00.2 E 135° 34' 05.7).
from Osaka to Kyoto the road goes up a hill, next to the usual river. Kyoto is beautiful and worth spent some days, you can stay at the student dorm for 200Y (1.5€), it's a dirty place but funny (Kyoto student dorm open to travelers GPS coordinates: N 35° 01' 41.5 E 135° 46' 42.2).
In the Japanese Alps in the first days of november starts to be cold in the night (a few degrees below 0°C) so we headed south to Mount Fuji without visting it (a pity), to rapidly reach Tokyo from the busy road that goes from Shizuoka. The only nice part here is the climb to Hakone, expect middle/heavy traffic though.