There’s something special about places on the outer limits of great nations or continents; a sort of liberated and reflective space, away from it all, yet still connected to it. Think Alaska, Vancouver Island, the Koh Chang islands in Thailand, Xining in far western China or the pearl of Sri Lanka hanging off the neckace of India.

Marine magic: Though off-limits to swimmers and divers, Kabira Bay is popular with visitors, who can go out in glass-bottom boats to view its gorgeous corals. However, at unrestricted Yonehara beach (above), a coral wonderland is just offshore.

On Ishigaki in the Yaeyama Island group, some 400 km southwest of Okinawa, there’s still a feeling of being in Japan, yet somehow it’s quite different and free from the magnetic force-fields of Tokyo, Nagoya, Osaka, Fukuoka and the rest.

Blessed with a warm climate, mountainous jungles and amazing beaches, Ishigaki seems to be in its own time zone, most intimately experienced by bicycle, tent and snorkel. Reached by direct flights from Tokyo or via Naha, Ishigaki — covering a mere 230 sq. km — is also easy to explore by rental car or by using a ¥2,000, go-anywhere Michikusa bus pass.

Arriving during a late-autumn storm, we had to organize our sightseeing around the weather.

In morning rain, we drove around the island, stopping at mangrove swamps teeming with fish and birds living among roots poking high up through the mud. Passing the untouristed northeast, we headed for the central mountains and Banna Park, rich with butterflies, flowers and strange plants.

Then, with clouds cooling the jungle air, it was a pleasure to make the short hike into the Yonehara Palm Tree Grove on the northern coastal slopes to see its array of species including the Yaeyama Palm, a designated national natural monument that’s found only on Ishigaki and on the neighboring Iriomote island.

After that, for ¥5,000 each, we could have joined a three-hour kayak tour along the Miyara or Fukido rivers. Scuba divers, however, may prefer to shell out ¥13,000 (plus ¥5,000 for gear rental) for two dives in the transparent ocean, getting in among the giant “flying” manta rays of so-called Manta Scramble just off the northern coast.

Fertile ground: Its wealth of vegetation is one of Ishigaki’s many attractions, from the Yonehara Palm Grove woods (left) to ferns such as this at Banna Park in the mountains.

But when the sun finally broke through, we had coral in mind and headed to Kabira Bay for a 30-minute, ¥1,000 tour in a glass-bottom boat. Perhaps Ishigaki’s most popular destination, Kabira Bay shines with jade and emerald green water rarely seen elsewhere. To preserve the reef, one of the few cultivation sites for black pearls in Japan, the bay is off limits for swimming, snorkeling and diving.

To experience the coral more intimately, we drove to nearby Yonehara beach. Surely one of Japan’s most delightful strands, Yonehara should be cluttered with hotels and condos and strictly enforced dictums about where to park and how to escape tsunamis. Instead, in typically relaxed Ishigaki fashion, we found broad-leafed plants sprouting willy-nilly from the sand — and even a swing hanging from a tree, perhaps put there by someone from the nearby campground.

Retail riot: A funky craft shop by a road in the north CHRISTOPHER JOHNSON PHOTOS

Close to shore, the reef is shallow enough for novice snorkelers, with space to walk in reef shoes around coral heads, away from stronger currents in areas posted with warnings. Unlike many beaches in southeast Asia, Yonehara seemed undisturbed by jet skis or tour boats. It was an awesome feeling to float in the surreal aquatic universe among fish passing like thoughts over brain coral — yet still have all the modern comforts of Japan to hand.

Back beaming with joy on the beach, we cuddled a poodle that came our way in between frolicking among snorkelers as if the beach was its yard. Then, after using the free showers, we drove past wind-sculpted roadside trees to Sukuji beach on the northwestern peninsula, to the Ishigaki Seaside Hotel. There, still high from snorkeling, it was sheer bliss to gaze inland from our room at near-Hawaiian mountain scenery, then look the other way across the sea and watch as the sun set in a blaze of orange and red.

For dinner, the Internet served up a great find in the Funa-kura no Sato restaurant on the west-coast road into Ishigaki town. With musicians singing and playing the local banjo-like sanshin, it was an Okinawan-style party atmosphere from the get-go, with outdoor and indoor tables and set meals of local fare priced between ¥2,300 and ¥5,500 per person. We decided to order a la carte, and so savored dishes including the salty local masu fish, at ¥1,500, inky-black ika-sumi squid risotto (¥800), mimi-ga pig’s-ear cartilage (¥500) and a range of local tofu (¥500), including one that was peanut-based. Completely stuffed, as we left to sample some island nightlife we felt like the puffy owl perched above us in a tree overlooking the parking lot.

Idyll: Sukuji beach from the Seaside Hotel

A number of restaurants feature Ishigaki steaks, which like Kobe beef, are marbled, rich and juicy. Among others, the Hotel Peaceland offers ¥2,500 set-lunch menus including 150-gram steaks — which go well with Ishigaki beer in its dark or “marine” (lager) versions. However, budget travelers staying at one of the hostels or family-runminshuku guest houses (where nightly room rates are ¥2,000 to ¥3,000 per person) might consider asking to cook where they’re staying, and shopping at local supermarkets. The port area also has ferries to nearby Iriomote and Taketomi islands, and sometimes — though erratically — to Taiwan.

Whatever your budget, though, on Ishigaki you’re sure to pick up the vibe of freedom and fraternity that pervades the whole island, especially when awamorifirewater is flowing in the downtown bars and izakaya pubs. Perhaps it’s because the island’s 45,000 residents — and visitors alike — don’t feel they have to conform to mainstream Japanese ways. Instead, it’s a place where rules are made to be broken, and where people act out of human kindness and go their own way.

But like many other paradises, Ishigaki faces threats to its purity. Conservationists are especially worried about Shiraho lagoon, on the less-visited eastern coast, where part of the Ryukyu Islands reef system there features the oldest blue coral in the northern hemisphere, as well as some 300 species of fish.

In the 1980s, when a planned new airport and land-reclamation project threatened the area, the World Wildlife Fund opened the Shiraho Coral Reef Conservation and Research Center, known locally as Shiraho Sangomura (Shiraho Coral Village). The airport project — set for completion in 2013 — was relocated inland, but many remain concerned about its environmental impact on this island where they claim construction projects are already damaging coral — and with it the attraction to tourists.

Despite ecological concerns, Ishigaki still maintains a wild natural beauty lost in so many other parts of Japan where the Construction State has poured concrete over mountainsides, riverbanks and the coastline. In fact, as you’ll hear many locals say — balance is the key. So go to Ishigaki with your hiking boots and snorkels — but slow down, relax, and enjoy the free and funky vibe at the far end of Japan.