There are 150284 bridges which are longer than 15 meters in Japan. Most of the bridges are built by steel or concrete, but there are 1209 stone bridges and 330 wooden bridges.
Most important bridge should be Nihonbashi which is the starting point of Japanese road network. Therefore distances between Tokyo and other cities are calculated from Nihonbashi in Tokyo.
Most popular bridge in Japan might be Togetsu bridge in Arashiyama district in Kyoto. Or Kintai bridge in Iwakuni, Yamaguchi prefecture which charge a small toll to cross the bridge.
Honshu island and Shikoku island is connected by 3 bridges and Honshu island and Kyushu island by 1 bridge. On the other hand, there is no bridge between Honshu island and Hokkaido island and between Shikoku island and Kyushu island. Honshu and Hokkaido is connected only by railway tunnel. Then, there is no tunnel between Shikoku and Kyushu either.
Therefore if you want to travel between Shikoku and Kyushu, you have to travel via Honshu or fly by airplane. However, please note that the air connections between Kyushu and Shikoku are not so convenient either.