Islands of Japan Worth Ditching the Mainland For

Man paddling in ocean under rainbow in Okinawa

Japan is an island nation. Now, please repeat with me – Japan is an island nation. And now, again, but this time in Japanese – Japan is a “shimaguni.” In his excellent book about Japan – Bending Adversity, David Shilling refers to the term shimaguni (島国)- meaning island country in Japanese, as “incantation,” as a magic term to end all conversations about Japan.

In a country where the desire to be unique, not individually, definitely not individually, but as a nation, is cherished above anything else, the sense of isolation brought on by being an island is often the answer to both good – authentic and unique aspects of Japanese culture – and bad – let’s say Japan may not be one of the flag carrier countries in terms of certain aspects of the societal progress (for my ramblings about Japan`s island-nationess: From an Isolated Island-Nation to that Place Where the Continents Meet). And I guarantee you, you will hear the word “shimaguni” at least once, even if you visit Japan for a short trip.

14,000 islands of Japan

Well, the societal aspects aside, Japan is indeed an island nation. In addition to its four main and largest islands—Hokkaido, Honshu (home to the country`s biggest cities, including Tokyo), Shikoku, and Kyushu—collectively referred to as the mainland, Japan is home to approximately 14,000 islands. You might read the news from last year, where it was reported that Japan had just discovered another 7,000 islands that are part of its territory that it had not been aware of before.

When you look at the map, some of these islands appear very tiny and evoke a hopeless sense of loneliness. But once you get there, they surprise you with the vividness of local life surrounded by wild nature, the kind that one cannot experience or easily access on the mainland. I have always been captivated by the allure of Japan’s smaller islands—the islands of an island—where one can truly feel the enigmatic sense of disconnection that only a combination of geological and mental isolation can bring.

In this post, I will list some of my favorite islands in Japan. These include tropical paradises that offer swimming experiences comparable to those on Thai islands, a hiking mecca that inspired Hayao Miyazaki for one of his most beloved animes, islands whose beauty hides their dark historical past, and many more.

Table of Contents

    Tokashiki Island: the unforgettable Kerama Blue

    Man walking on a beach in Tokashiki Island in Japan

    Tokashiki Island, belonging to the Kerama Islands group, is my favorite summer destination in Japan. Located merely 30 minutes off the coast of Naha, the main city of mainland Okinawa, Tokashiki Island is home to two main beaches and two very small settlements. Aharen Beach is where the action happens with a wide range of daytime eateries and water sports centers – whereas Tokashiku Beach is the place to go for a quiet and relaxing beach time.

    I try to visit Tokashiki every summer. I stay at the same hostel – old but very well-maintained Kerama Backpackers, which charges around USD 25/night for a dormitory bed. Every morning, I go to the same lovely and only breakfast place on the island to have my sandwich and two cups of coffee.

    I then walk to Tokashiku Beach, where I spend at least half of the day, if not more. With a cove-like setting and lush greenery right behind the beach, it reminds me of Koh Tao in Thailand. I sometimes walk to Aharen Beach at lunchtime to have a sashimi donburi from the second-floor terrace of the local eatery overlooking the beach. While the weather is usually very hot and humid, there are also a couple of hiking trails that start near Aharen Beach, with viewpoints offering different versions of the same mesmerizing ocean scenery. In the evenings, I go to the same (and only) yakitori place on the island.

    I try to do this every summer for 4-5 days, and I am looking forward to repeating it this coming summer, hopefully in August or early September.


    Zamami Island: where the divers go

    Kayak facing beach on ocean in Zamami Island Okinawa

    Also a member of the Kerama archipelago, Zamami Island is a heaven for divers and snorkelers. Similar to Tokashiki, Zamami is also home to two main beaches, Ama and Furuzamami Beaches. Ama Beach is very popular for stand-up paddling (SUP) and is home to one of the nicest ocean-side public camping grounds in Japan. Zamami is also a good place to join guided kayak tours that take you to parts of the islands you may not be able to access on your own.

    Despite its small size, Zamami Island has a good range of eateries, including food cart-style ones that pop up near the beach right before sunset.

    For more about Tokashihi and Zamami: Kerama Blue: Tokashiki and Zamami Islands in Okinawa


    Yakushima Island: mystical island home to Japan`s oldest tree

    Fog over mountains in Yakushima Japan

    Yakushima Island, one of the two first UNESCO Heritage Sites in Japan, needs no introduction. It reached the height of its popularity as a place that inspired Hayao Miyazaki for his famous anime, Princess Mononoke. The island is famous for its hiking trails, moss forests, and ocean-side onsen. Yakushima is also home to Japan`s, if not the world’s, oldest tree—Jomon Sugi, estimated to be 2,200-7000 years old. The hikers flood Yakushima every holiday season to hike the 10-hour Jomon Sugi trail to pay their respects to this impressive tree (and to get their certificate).

    My favorite hike in Yakushima, where I was once lucky enough to stay for almost three months, is the hike to Mount Miyanoura, the highest peak of Kyushu. The mountain, which can be climbed as a (long) day hike or multi-day one if you want to combine it with other trails, including Jomon Sugi, represents the impressively diverse landscape that the island is home to; every section offers unique scenery and plant diversity, reminding you all the reasons why the island is inscribed as UNESCO Heritage.

    If you have plenty of time and have already done the rightfully popular hikes, such as Shiratani Unsuikyo—home to the famous moss forest—and are looking for a less conventional hike/walk, you can also circle the heart-shaped island, following the 100-kilometer ring that surrounds it. Part of the road will take you through Seibu Rindo Forest Path, the beloved home of the island`s monkeys and deers. I did the walk in two nights and three days and thought it was a wonderful opportunity to explore the tiny seaside communities of the islands that could otherwise be overlooked.

    For more about Yakushima: Hiking Mount Miyanoura, In Praise of Road Walks: Circling Yakushima, and Yakushima: Land of Beautiful Hikes


    Sadogashima Island: controversial history but a remarkably vivid daily life

    Sadogashima, located off the coast of Niigata in the eastern part of Japan, was one of the most surprising trips that I ever had in this country. I visited the island in the summer of 2023 after having to cancel a week-long trip to Hokkaido due to torrential rain caused by a typhoon. Sadogashima was one of the only places in Japan with a promising weather forecast.

    This second-largest island, after Okinawa, outside of the four main islands of Japan, turned out to be a remarkable destination worth a week-long trip of its own. With picturesque rice paddies, small villages where narrow alleys always lead to the ocean, historical sites, and a beautiful mountain traverse hike, Sadogashima far exceeded all my expectations. I benefited from a tourist bus pass to explore the island, including Onogame, which is famous for its 167-meter monolith overlooking the ocean and daylilies that bloom in late May. I stayed at the wonderful Hostel Perch located in lovely Kawaharada town, home to local and atmospheric izakayas and a deliciously inviting sushi place run by a family, all within a few minutes of a beautiful beach.

    I also spent a day hiking the island’s mountains, which offered beautiful but uniquely strange scenery that could only be Japan. For more: Sadogashima Island Traverse Hike: Forests, Ridges and Strange Things.

    The island is also home to Sado Kinzan, Japan`s most productive gold mine during the Edo Period, which is today open to visitors as a museum. The site—currently being reviewed for UNESCO Heritage listing—is a matter of big controversy between Japan and South Korea, with the latter claiming that many Koreans were the victims of forced labor in this mine during World War II. Japan`s nomination of the site as a World Heritage without any acknowledgment of these claims has revived the controversy.


    Amakusa Islands: the islands of prayers

    I visited the Amakusa Islands many times for writing assignments. The group of 120 islands, also referred to as the “islands of prayers,” lies off the coast of Kumamoto Prefecture in Kyushu.

    While the archipelago stands out as a unique nature destination—qualifying as a geo-park—I have always been more intrigued by the islands’ history, which is connected to the Hidden Christians of Japan and the largest civil conflict in the country`s history—the Amakusa-Shimabara Rebellion.

    In 1637-1638, the villagers who were imposed to overtaxing practices of the military rulers of the period and the Christians living in fear of persecution (Christianity was banned in Japan during that period) revolted against the government under the leadership of a native of Amakusa, who was only 16-years old at the time. The rebellion was eventually – with the help of the Dutch – suppressed by the government, but it marks a milestone event in the history of Japan.

    Today, there are many sites on the islands linked to the Amakusa-Shimabara Rebellion and the Hidden Christians of Japan. Sakitsu is one of the most picturesque villages of the Amakusa Islands and also culturally the most significant one. Designated as a UNESCO World Heritage site in 2018, the village played a central role in the spread of Christianity in Japan following the introduction of the religion by Portuguese priest Luis de Almeida in 1569. The fishing hamlet was home to thousands of Hidden Christians who practiced their religion in secret for more than two centuries. In 1888, 15 years after the ban on Christianity was lifted, Sakitsu welcomed its long-desired first proper church, built on the site where once the Hidden Christians were forced to renounce their faith by stepping on a stone featuring the figure of Jesus or Mary—the infamous fumi-e practice depicted vividly and horrifically in Martin Scoreses`s 2017 feature film, Silence.


    Goto Islands: intriguing history and mesmerizing nature

    Reflection of christian church on water in Goto islands in Japan

    Another group of islands that hosts many sites related to the history of Hidden Christians of Japan is the Goto Islands, located off the coast of Nagasaki on the island of Kyushu. One of my favorite destinations in Japan, along with Nagasaki City, Goto is a group of five islands that each offers a perfect blend of nature and history.

    Fukue and Nakadori Islands are the largest two islands in the group, and each offers a wide variety of accommodations and eateries. Thanks to the ferry service, island hopping is possible, but I highly recommend that you spend at least a few nights on each island. Both islands are home to many Christian churches, some of which are listed as UNESCO Heritage.

    In March 2024, I posted daily diaries during my second visit to Goto Islands on Substack. You can refer to #traveldiaries on Substack or read it as a single piece on my website: Walking Goto Islands.


    Ojika Island: stay with the locals

    Two tori gates facing the sea in Ojika Island in Japan

    While merely 35 minutes away from Nakadori Island in the Goto Islands chain, Ojika Island is not only administratively part of the Goto Islands group but also has a very different vibe.

    Home to 2,300 residents, Ojika is a place to experience the rural, and I mean very rural, side of Japan. The island is very popular among Japanese locals and foreign tourists for the homestay experiences offered by the islanders. There is also the option of kominka-style accommodation, where the guests can have the entire old but stylishly renovated Japanese home to themselves.

    On Ojika Island, I stayed at the wonderful Ya no Ya, run by a lovely young couple who renovated a century-old Japanese house. We cooked and ate together. After a day of exploring and sightseeing, I was each evening looking forward to coming back “home.” After a sightseeing-filled week in the nearby Goto Islands, Ojika served as a wonderful base to have a little bit of chill time and take things slowly, very slowly.


    Nozaki Island: maybe a little eerie, but a truly memorable island

    A wild deer looking at the camera in Nozaki Island in Japan

    Nozaki Island is a popular side trip from Ojika. The island is home to the picturesque Nokubi Church and the ruins of an old village, both of which are registered as UNESCO World Heritage Sites and as one of the 12 Hidden Christian Sites in the Nagasaki Region.

    The island, once home to 650 residents, currently has only one (temporary) human resident. But do not worry; there are approximately 400 wild deers – usually hanging around in a savannah-like part of the island – that will keep you company.

    In addition to a Nokubi Church and the abandoned village, there is also a hiking trail that leads to a Shinto shrine.


    These are some of the islands in Japan that I love visiting, often repeatedly. While the mainland has plenty to offer, those who have the time may consider exploring these islands to experience a side of Japan that cannot be seen on the mainland.