The rainy season is usually not a preferred travel season in Japan.
However, here are my 8 reasons why you should visit Japan during the rainy season!

① Everyone avoids Japan.
① The sightseeing spots are not that crowded.
① Hotels and flights might be cheaper than in Sakura season or autumn leaf season.
① It is not too cold and not too hot.
① There are still not as many mosquitoes as in summer and autumn!
① It is not raining every day, you might get a week full of sunny weather!

① The Hydrangea bloom is wonderful! You should visit famous Hydrangea spots! (But be sure to visit on a rainy day. It is crowded otherwise..)
① Japanese gardens are the most beautiful in the rain!
The green is shining, the moss is green and you will have a very special atmosphere.
It is hard to explain… But when you once sat down in a tea house at the open door and watched the garden while rain dropped on the roof and created a soothing sound, you will know what I mean.
So what.. I love the rainy season!
You should try!

Places to visit (in Tokyo and Kanagawa + Shimoda):
Meigetsu-in temple in Kamakura (Kanagawa prefecture)
Hasedera temple in Kamakura (Kanagawa prefecture)
Kaisei town Hydrangea Park (Kanagawa prefecture)
Hakusan shrine(Tokyo)
Shimoda city Hydrangea Park (Shizuoka prefecture)
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Hasedera, a modern temple in Kamakura
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Meigetsu-in, the Hydrangea temple in Kamakura
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Related content:
Hydrangea and it’s language
The most popular plants in Japanese private gardens