In places where land submerges itself beneath water, modes of transportation immediately change and, in some cases, endings become beginnings.

The Kintetsu Line train to Toba in Mie Prefecture deposited me practically in front of Ise Bay, which is less known for its fish than for its artificial-pearl industry. The absence of sea-facing shrines suggested that the waters here were calmer than in the open sea, minimizing the need to erect dedicatory sites to protective sea deities.

Calm waters, as I soon found out, are essential for pearl cultivation. The best place for a crash course in this extraordinary process is the museum on Mikimoto Pearl Island, a short walk across the Pearl Bridge from Toba Station. The well-labeled displays, models and lifelike figures explain how pearl production is conducted out among the oysters. The use of words connected to agriculture, the talk of “seeding” and oyster “grounds,” is telling, as while this may be a man-made process, there is a decidedly organic aspect to it.

Nacre, a pearly substance, begins to secrete after a segment of mantle lobe is carefully transplanted into oyster tissue. More liquid begins to be secreted within a one- to two-week period after a sack has started forming around the nucleus of the future pearl. As layers of calcium carbonate in minute crystalline form are deposited in concentric layers, a pearl is created.

This is an exhausting process for the host molluscs, requiring a period of recuperation in which the newly created jewels are left to soak in sheltered waters. They are then transferred to rafts situated close to the mouth of bays. These rafts, forming pleasing geometrical webs as seen from the surface, were to become a familiar sight over the next couple of days. More powerful currents guarantee exposure to flows of enriching plankton. If you peer below the raft frames, you will see oyster baskets suspended there.

With the advent of winter, the baskets are placed in slightly warmer waters (above 10 degrees), then before their pearls are harvested the oysters are taken to waters that can improve the jewels’ luster. Ama (women oyster or abalone divers) are still employed in these areas to recover the pearls. Photo books dating from as recently as the 1970s show the women diving, then emerging bare-breasted and smiling from the water — an implausible sight in these less innocent, more self-conscious days.

A more intimate look at pearl cultivation is possible by visiting the quieter climes of Kashikojima, the terminus of the railway line. Initially, I had little sense of being on an island. It was only on the next day, when I retraced the route on foot, walking over the bridge linking it to the mainland, that the landscape slowed down and its features fell into place, making sense out of the blur of speed accompanying my arrival.

The station is situated a little short of the small port, a single street terminating at the waterfront. In 1920, the line, then known as the Shima Electric Railway, was extended to the island. Back then Kashikojima was uninhabited. Shards of pottery and ancient tools have been found there, but quite why such a sheltered beauty spot was ever abandoned before the advent of the railway remains a mystery. The line helped to revitalize the island, but even in summer the volume of tourism remains moderate, the bay known only to a small cognoscenti of mostly Japanese visitors.

One early exception to Kashikojima’s relative obscurity was a visit to the island by the English travel writer Ethel Mannin, who stayed there in 1959. In her Japan travelogue, “The Flowery Sword,” she wrote, “Kashikojima is perhaps the most beautiful place in the whole of that beautiful area which comprises Ise-Shima National Park. It must surely be one of the most beautiful places in all Japan.”

Somehow the island conspires to be both grand and diminutive. With a circumference of little more than 7 km, and with few sites or structures of historical interest, it and its surrounding waters are best appreciated for their natural features. The sweeping views of the bay contrast with the constricted station and quay area — though the spatial restrictions have at least meant the area has been seen as too confined to develop or tinker with.

One building of distinction is Matsui Pearls, a showroom built in 1905. The wooden structure, with its original signboard, stands opposite the quay where fishing and cruise boats are moored.

If you want a good view of the bay, something like a panorama, you either have to stick to the high ridges above the port or board a boat. There is a large hotel on the hill behind the settlement, the luxurious Shima Kanko Hotel, renowned for its nouvelle cuisine, tastefully landscaped gardens and fine views. But there is nothing quite like being down by the bay itself and staying at one of the waterfront minshuku (family-run guesthouses) around the port, where the life of the shoreline and countless islets is more visible and more deeply felt.

I opted to seek out the quietest sanctuary of all, a traditional inn called the Ryokan Ishiyama-so on the tiny island of Yokoyama. There is no public transport to the islet, a stay there requiring a phone call from the quayside and a short wait until its owner comes to pick you up in a small launch.

The inn is convincing proof that a water passage, even of 3 or 4 minutes, can be transfiguring. The friendly couple who run the establishment were once great devotees of Bali, until the Indonesian isle became simply too commercialized for their tastes. Disillusioned with its rampaging materialism and the erosion of once-tranquil villages and landscapes, they decided to re-create in Ago Bay the faraway setting they had loved.

What might in other hands have degenerated into an exercise in kitsch, here works rather well. In something akin to what you might once have found at a waterside Balinese hamlet, the visitor enters a spacious reception area replete with tropical plants, rattan furniture, piped gamelan music and a broad wooden waterfront deck.

Of a summer evening when the tour boats are moored, the outline of hills has receded into darkness and barely all that remains are the silhouettes of pearl rafts floating on the flaming red water, there is something almost Southeast Asian about the ambience — particularly when your host places a bottle of iced Bintang Beer in your hands. Don’t expect to savor gado-gado, sambal or rijsttafel here, though. Dinners at the inn and in the minshukus at the port consist of copious amounts of some of the freshest seafood dishes you are likely to come across.

There are no beaches, easily accessible interior nature reserves or forests on the island, making it a cumbersome process to get around on foot. Lanes often terminate in chain-link fences, indicating private property. Paths tend to end in similar barriers, or to descend to fallow or weed-infested plots — or to quiet, little-visited pearl operations. A handful of workers were taking a nap when I emerged at one such place, one person snoring in a cot, the others supine across a floating pearl raft. It was a scene of somnolence, a stolen siesta from an otherwise brisk day of activity.

To truly appreciate Kashikojima and the islets here, the luxuriant greenery of its shoreline and the details of the pearl farming that sustains the region, you have to get out into the bay on a boat. The smaller vessels that offer short trips around this waterworld provide a close-up, more intimate view of what’s going on; the boats chugging gingerly between pearl rafts and fences, where men and women work from small huts built on the timber frames. This more proximate view reminds you how much life there is in the bay, both marine and human.

An alternative to the converted fishing boats is a replica of a Spanish galleon that plies these waters in similar fashion to the one on Lake Ashino-ko (aka Hakone Lake) beneath towering Mount Fuji in Kanagawa Prefecture. A visual anomaly, the vessel has one advantage, which is the elevated view from its high deck. It’s a little like being moved around the bay on a crane, each turn of the boat offering a fresh perspective.

A half-century ago, Ethel Mannin could never have envisaged a faux Spanish galleon or Balinese guesthouse, but in most other respects, she would have no difficulty recognizing the bay as it is today, or the profound stillness of its woods and waters.

Travel tips: Kashikojima is the terminus of the Kintetsu Line linking it to Nagoya, Osaka and many other stations. The Annaijo (Information Center) there has maps of the area and can arrange accommodation. Ryokan Ishiyama-so (0599-52-1527) is 3 or 4 minutes by boat from the quay.

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