When most people think of Japanese islands, they picture Okinawa, maybe Hokkaido. If they are really into travel, they might know about Yakushima or Naoshima. But Japan is an archipelago of nearly 7,000 islands, and scattered among them are places so remote, so strange, and so beautiful that even many Japanese people have never heard of them. I have spent years tracking down Japan’s most obscure islands, and these five are the ones I keep telling people about.
1. Aogashima: The Volcanic Island Inside a Volcano
Aogashima is, without exaggeration, one of the most visually striking places I have ever been. It is a volcanic island about 360 kilometers south of Tokyo in the Philippine Sea. The entire island is a double caldera: a large outer crater with a smaller volcanic cone sitting inside it, surrounded by lush green walls. From above, it looks like something from a science fiction film.
The population is roughly 170 people, making it the smallest village in Japan. There is one school, one restaurant, and a few minshuku (guesthouses) charging around 6,500 to 8,000 yen per night with meals. The island has a geothermal sauna where volcanic steam heats a natural rock room (free), and residents use the steam vents to cook eggs, potatoes, and other food in what they call “hingya” cooking.
Getting there is the adventure. There is no airport. A helicopter from Hachijojima (another remote island reachable by plane from Haneda, about 55 minutes, around 14,000 yen one way) runs once daily with nine seats. The alternative is a ferry from Hachijojima (around 3,000 yen) that runs three to four times a week and is frequently cancelled due to rough seas. I waited two extra days on Hachijojima once because the ferry could not dock. Plan for flexibility.
Once on Aogashima, you can hike around the caldera rim, visit the inner volcanic cone, stargaze (the lack of light pollution makes it one of the best stargazing spots in Japan), and experience a way of life that feels detached from modern Japan. There is limited cell phone service and no convenience stores. Bring cash and an open schedule.
2. Megijima: The Island of Demons
Megijima sits in the Seto Inland Sea, just 20 minutes by ferry from Takamatsu in Kagawa Prefecture (round trip 740 yen). Despite being so accessible, most tourists skip it entirely, heading instead to the more famous art islands of Naoshima or Teshima. Their loss.
Megijima is said to be “Onigashima,” the Island of Demons from the famous Japanese folktale Momotaro (Peach Boy). At the top of the island, a massive cave complex (admission 500 yen) has been decorated with oni (demon) statues reenacting scenes from the story. It is kitschy, strange, and genuinely fun, especially if you know the tale.
But the real magic of Megijima is the island itself. The village is a collection of old stone-walled houses, many abandoned, now gradually being reclaimed by nature. During the Setouchi Triennale art festival (held every three years, next in 2028), artists install works throughout these empty houses and the island’s landscape. Even outside the festival, some permanent installations remain.
The island has a small beach, a lighthouse hike with panoramic Seto Inland Sea views, and a quiet, slightly eerie atmosphere that feels nothing like mainland Japan. There are a couple of small restaurants and cafes, but hours are unpredictable. Bring snacks. You can explore the entire island on foot in three to four hours.
3. Rebun Island: The Flower Island at the Edge of Japan
Rebun sits off the northern tip of Hokkaido, closer to Russia than to Tokyo. It is called the “Island of Flowers” because its alpine meadows bloom with wildflowers from May through September, despite being at sea level. Species that normally grow only at high elevations thrive here because of the cold northern climate and sea winds.
The island’s main attraction is hiking. The Rebun Island 8-Hour Hiking Course runs along the west coast, passing through flower fields, along dramatic sea cliffs, and through tiny fishing villages. It is one of Japan’s finest coastal hikes. The Cape Sukoton trail (about 2 hours) at the island’s northern tip offers views toward Sakhalin on clear days.
Getting there: fly from Sapporo to Wakkanai (about 55 minutes, from 10,000 yen one way) or take the JR Soya Line (about 5 hours), then a ferry from Wakkanai to Rebun (about 2 hours, 2,800 yen one way). Accommodation is mostly minshuku and pensions, from around 7,000 yen per night with meals. The seafood on Rebun is exceptional, particularly uni (sea urchin) from June through August. Uni-don (sea urchin rice bowl) at local restaurants runs 3,000 to 5,000 yen, and the freshness is unmatched.
Visit between late June and mid-August for peak flowers. The island is cold and windswept, even in summer. Bring layers and rain gear.
4. Ojika Island: Forgotten Japan in the East China Sea
Ojika is a small island in Nagasaki Prefecture, part of the Goto Islands chain in the East China Sea. It has a population of about 2,300, a handful of historic villages, and virtually zero foreign tourism. I stumbled across it while researching the “Hidden Christian” UNESCO World Heritage sites, and it turned out to be one of the most peaceful places I have visited in Japan.
The island has two UNESCO-listed hidden Christian sites: the former Nozaki Island settlement (reached by charter boat from Ojika) and the Kyurokusaki Church. For centuries, Christians on these islands practiced their faith in secret during the long prohibition period (1614 to 1873), hiding religious artifacts inside Buddhist altars and developing unique prayers that blended Latin with Japanese.
Beyond the historical sites, Ojika is simply a beautiful, quiet island. The old town has well-preserved Edo and Meiji-era buildings, some converted into guesthouses by the island’s revitalization NPO. Staying at one of these restored kominka (traditional houses) costs around 5,000 to 8,000 yen per night and offers an experience of rural Japan that has largely vanished on the mainland.
Getting there: ferry from Sasebo (about 3 hours, around 3,500 yen) or from Hakata (Fukuoka) by overnight ferry via the Nomo Shosen line. The island has a few restaurants, a couple of small shops, and rental bicycles (around 500 yen per day). Cycling the island takes about three hours and passes through rice paddies, fishing harbors, and quiet beaches where you might be the only person.
5. Iriomote: The Japanese Jungle Island
Iriomote is part of the Yaeyama Islands in Okinawa Prefecture, closer to Taiwan than to mainland Japan. About 90 percent of the island is covered in dense subtropical jungle and mangrove forest, and it was designated a UNESCO World Heritage site in 2021. This is Japan’s wilderness island, and it feels more like Southeast Asia than anything you associate with Japan.
The island is home to the Iriomote wildcat, one of the world’s rarest wild cats with only an estimated 100 individuals. You are unlikely to see one (they are nocturnal and extremely shy), but you will see their crossing signs on every road.
The main activities are river kayaking through mangrove forests, jungle trekking to waterfalls, and snorkeling. Kayaking the Urauchi River to Mariyudu Falls (a two-hour guided trip plus a 40-minute hike) costs around 8,000 to 12,000 yen with a guide, and the combination of paddling through mangrove tunnels and then hiking to a jungle waterfall is unforgettable.
The Hoshizuna no Hama (Star Sand Beach) on the north shore has sand made of tiny, star-shaped shells from single-celled organisms called foraminifera. You can see the individual stars with the naked eye.
Getting there: fly to Ishigaki Island from Tokyo (about 3.5 hours, from 15,000 yen one way), Osaka, or Naha, then take a high-speed ferry from Ishigaki to Iriomote (about 40 minutes, around 2,060 yen one way). Accommodation ranges from simple guesthouses (4,000 to 6,000 yen) to resort-style hotels (15,000 to 30,000 yen). Book activities and accommodation well ahead during summer (July and August).
Quick Tips for Japan’s Remote Islands
Ferry schedules rule your life. Ferries to small islands run once or twice daily and cancel frequently due to weather. Always have a buffer day in your itinerary.
Cash is essential. Many islands have no ATMs, or the ATM does not accept international cards. Bring enough cash for your entire stay plus a buffer.
Bring supplies. Sunscreen, medications, insect repellent, and snacks may be unavailable or very limited on small islands. Convenience stores are rare or nonexistent.
Communication. Cell service can be spotty on remote islands. Download offline maps and have accommodation addresses written down before arriving.
Respect the environment. Many of these islands have fragile ecosystems. Follow trail markers, do not take shells or rocks, and pack out all trash.
Japan’s remote islands are for travelers who want to see what happens when you go past the last train station, past the last convenience store, past the last point where the guidebook has anything to say. The reward is a Japan that most visitors never experience: wild, quiet, ancient, and strange. Pick one island, build some extra days into your schedule, and go. The best travel stories start where the itinerary ends.
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