I am interested in those pyramids and hammerheads in Yonaguni too, just wondering if it is possible to go to Yonaguni from Taipei? I heard that it can only be reached from Naha.
I have been to Yonaguni. It is a quant little island with wild horses and cows. On a clear day you can see Taiwan, so it should be easy to take a ferry or fly to Yonaguni.
Also known as Dunan (どぅなん

in the local language, Yonaguni is a tiny speck of an island (28 sq. km.) with a population of less than 2000, located 125 km from Taiwan and 127 km from Ishigaki. The main population centers are Sonai (祖内

on the north coast, Kubura (久部良

on the west coast and tiny Higawa (比川

in the south. The total population is about 1700.
Although it lacks the resorts of the larger Yaeyama islands and its few visitors are mostly divers coming to witness the island's mysterious sunken ruins and hammerhead sharks, the island has beautiful (yet uncrowded) beaches, cultural attractions, and various mysteries of history.
Yonaguni is among the remotest inhabited spots of Japan and getting there is both inconvenient and expensive. Both flights and ferries may be cancelled at short notice if the weather is bad (particularly around typhoon season), so allow some buffer in your plans.
[edit] By plane
Expanded in 1999 to allow jets to land, tiny Yonaguni Airport (OGN) fields 1-2 flights daily from Ishigaki on Japan Transocean Air and Ryukyu Air Commuter (30 minutes, ¥10000/17000 one-way/return), and RAC flights 3 times a week from Naha.
[edit] By ship
Fukuyama Kaiun (福山海運

, tel. 0980-87-2555, runs boats from Ishigaki on Wednesdays and Saturdays, with return trips on Mondays and Thursdays, always departing at 10 AM. The trip takes four hours on a good day and costs ¥3460/6580 one-way/return; note that most of the journey is across the open sea and people prone to seasickness may wish to steer clear. A cargo boat also offers an irregular (unscheduled) service to Naha.
Star Cruises discontinued their Keelung (Taiwan)-Yonaguni cruises in 2006, but they seem to be back in business as of November 2007. Contact them at the link above if you're interested in arriving from Taiwan.
Capes, cliffs and beaches
Marker for the westernmost point in Japan, Cape IrizakiCape Irizaki (西崎

. Yonaguni's main aboveground sight of any interest is the marker for the westernmost point of Japan (日本最西端の碑

, located here at the westernmost tip of the island, about a kilometer from Kubura (15 minutes on foot).
Cape Agarizaki (東崎

, at the east tip of the island. The kanji mean East Cape, but the reading of the name refers to the rising sun. You can observe it from a cliff. On a clear day, if you're lucky, you can see the coast of Iriomote. Also a grazing area, many Yonaguni horses can be found here.
Kuburabari (久部良バリ

. This cliff near the northern side of Kubura's port offers views of the last sunset in Japan, and on a good day it is possible to see the shadow cast by Taiwan in front of the setting sun from here. This is also the site where, in the rough period when residents of the island were forced to pay an alarmingly expensive head tax after the Ryukyu Kingdom was conquered by the Satsuma clan from the Japanese mainland, pregnant women were sometimes made to jump to their death to avoid an increase in population.
Ubudumaihama (ウブドゥマイ浜

. From the cliffs here, there's an impressive view of much of Yonaguni's beautiful northern coastline.
Hikawa Beach (比川浜 Hikawahama). Located on the southern shore of the island in Hikawa. Shaped like a crescent, it is the island's largest beach. Suitable for swimming. Very quiet, little to no waves because of a coral reef.
[edit] Rock formations
Kuburadake (久部良岳

. Kuburadake is a Natural Conservation District in the west of Yonaguni, about 188m above sealevel. It is valuable because it contains both a Chinquapin mountain forest and a lowlands forest, home to such natural monuments as the colorful Emerald Dove (リュウキュウキンバト

, Japanese Wood Pidgeon (ヨナグニカラスバト

, Ryukyu Robin (ウスアカヒゲ

, and others. From about halfway up the mountain to the summit, the trees are mostly date palms. Lower than halfway, you can find Javanese bishopwood trees (アカギ

and other diverse plants which the Atlas moth eats.
Tindabana (ティンダバナ

. Tindabana is a natural rock formation with a nice view. About 70m tall. From Tindabana, you can see the entire village of Sonai, and Nandahama. According to tradition, the great empress of Yonaguni, Sanai Isoba, resided here.
The following rock formations are best viewed by boat.
Gunkan-iwa (軍艦岩

. The "Battleship Rock", about 2km south of Agarizaki, is a series of peculiarly-shaped reef rock formations. Supposedly, the main rock bears a close resemblance to the shape of a battleship, and that's how it got it's name. It can be observed from Sanninudai.
Sanninudai (サンニヌ台

. Believed by some to be an above-water portion of the mysterious undersea ruins because it is shaped almost like a sort of stairway. The strangely-shaped rocks of Gunkaniwa can be easily seen from here. Also, there's a rock here with some writing on it which is mysterious. It bears little resemblance to kaida-dii, the island's indigenous writing system, and some have even suggested that it is Phoenecian.
Tatigamiiwa (立神岩、タティガミイワ

. The "Standing God Rock", at the southeast tip of the island, is also noted for the underwater ruins nearby (see Do, some with what appears to be indigenous writing. Also, it's considered a spiritual site for followers of Yonaguni's indigenous traditional religion.
[edit] Culture
Yonaguni Ethnographic Museum (与那国民族資料館 Yonaguni Minzoku Shiryōkan, literally "Yonaguni Ethnicity Information-center"). This museum, at No. 49 in the Sonai area, is run by 87-year-old "island auntie", Ikema Nae. There's a lot of information about the island's history, culture, and even language. If you want information about the island's indigenous writing system, kaida-dii, this is probably the place to go. Their informational pamphlets can also be very enlightening, but they are only occasionally offered in English. The museum also sells the Dictionary of the Yonaguni Tongue (与那国語辞典 Yonaguni kotoba jiten), the only available dictionary of the local language (to and from Standard Japanese), also with a little bit of information about the native writing system. Incidentally, the dictionary is written by Ms Nae, and the entire museum is mostly the result of her work. If you have any questions, she's usually there and is very knowledgable about the history, culture, language, and traditions of Yonaguni.
Bullfights (闘牛
[edit] Fauna
The island's unique fauna are also of interest.
Yonaguni horse (ヨナグニウマ yonaguni-uma). Bred in isolation on Yonaguni over hundreds of years, the Yonaguni horse is a very small breed, only about 10 hands high (100 centimeters/3.5 feet). Nowadays, most are wild, in two free-ranging herds (about 108 horses total). They're generally very tame and gentle, thanks in large part to the kind treatment they receive from the islanders. You'll probably see at least one if you're on the island for very long.
Atlas moth (ヨナグニサン yonaguni-san). The largest known species of moth in the world. Although it can be found in other parts of Asia (mostly in Taiwan, India, and Malaysia), the first specimen was collected in Yonaguni and they are abundant. The Atlas Moth Museum (アヤミハビル館 ayamihabiru-kan) southeast of Sonai (tel 0980-87-2440) has live caterpillars in season as well as various displays of local insects and other critters. You won't be able to see the adult moths, though, as the cocoons are returned to the forests.
Anbonia (アンボイナ amboina). A very beautiful but also very poisonous seashell. See here for more information on how to watch out for them.
[edit][add listing] Do
Scuba diving is without a doubt the main draw for most visitors to Yonaguni. However, the island's location in the middle of the open sea without protective reefs means that waves can be high and currents can be strong, so most diving here is drift diving and many of the more interesting dive sites are only accessible to experienced divers.
Yonaguni Diving Service. Kubura, tel. 0980-87-2658, [3]. The oldest and largest dive shop on the island, quite professionally run: they will cater to your experience level and will not head out to sites if the weather does not permit (in which case your money is refunded). Two boat dives start from ¥12,000, full gear rental for a day is ¥6,500. No credit cards accepted and only limited English spoken. Quite popular, so book ahead.
[edit] Underwater ruins
Exploring the underwater ruinsYonaguni's unique attraction for archaeologists and divers alike are the mysterious underwater ruins (海底遺跡 kaitei iseki) which lie off the southern coast of the island. A single platform 100 by 50 meters wide and up to 25 meters tall, seeming carved out of solid rock at perfectly right angles and dated by some to be 8000 years old, the technology required to build them here doesn't seem to match any known timeline of human history. Some maintain that they are the product of the lost Continent of Mu or even alien artifacts, while the most boring explanation would be that they are merely the product of strange geological processes although the (apparent) hallways and staircases, as well as what appear to be regular rows of holes dug for moving rock and even what some take to be a form of writing on the walls, would appear to defy this.
Seeing the ruins, however, takes some time, effort and skill: the area is notorious for its currents and not suitable for beginning divers, although several diving shops run one-day crash courses that culminate in a guided tour of the ruins. For those with the requisite skills (PADI AOWD or more), a day's diving starts at ¥12,000. Note that the ruins, some 20 minutes by boat from Kubura, are usually only accessible when they are on the leeward side of a north wind and the currents are not too strong, so you'll also need some luck just to get here.
Wind conditions permitting, SAWES can also arrange glass-bottomed boats to make the trip for ¥5000/head if there are five or more passengers (or you can charter the whole boat yourself). Don't expect to see very much, however, as the ruins are at a depth of 5 to 20 meters.
[edit] Sharks
In addition to the ruins, Yonaguni is also famous among Japanese divers for its hammerhead sharks, which congregate around the island and can be spotted on most dives in the cooler winter season (December-February). Yonaguni is also pretty much the only spot in Japan where it is possible to spot the giant whale shark, the largest of them all, although sightings are quite rare.
[edit] Caverns
Much of the southern coastline is dotted with caverns, caves and underwater rock formations, which make for spectacular but, again, slightly challenging diving. Daiyati and the Temple of Light are particularly well-known spots that bear more than slight resemblance to Swiss cheese.
[edit][add listing] Buy
The most popular Yonagunian souvenir by far is hanazake liquor, see Drink for details.
Ōasa Shoten (大朝商店

. One of Kubura's two general-goods stores. Has a pretty good range of hanazake tucked away in the back.
Yonaguni Kaien (与那国海塩

[5]. Located near the beach in Higawa, this store sells salt harvested from Kuroshio Current. The best stuff comes in big crystals several millimeters in size, and supposedly tastes somewhat sweet.
[edit][add listing] Eat
While there are a few small restaurants in Sonai and Kubura, most visitors opt to eat breakfast and dinner at their lodgings and lunch at their diving service.