Though not too well-known outside Japan, Yakushima is a popular destination for Japanese tourists, hence the infrastructure (hotels, restaurants, transportation) is good.
Yakushima (circumference 135 kilometers) is a small, nearly round granite island that has an area of ~505km2 and is mountainous with a number of mountains rising over 1,800m, including Miyanoura-dake at 1,935m and Nagata-dake at 1,886m. (JNTO, 2007) These mountains catch a great deal of precipitation, earning Yakushima a reputation of being one of the most rain-soaked places in Japan, with measurable precipitation 50% of the days of the year.
Due to its isolation, steep terrain and exceptional climate Yakushima is one of Japan's natural wonders. The rocky coastline and the verdant mountains rising sharply in the center of the island are often spectacular. Wildflowers and blossoms decorate roads and forest. The pink sunrises and blood red sunsets over the Pacific are breathtaking. White clouds line the horizon and pile up billowing in the blue sky. Mists and rain clouds shroud the tops of the mountains. When the moon has set, the night sky is black and entirely filled with stars.
The island's forests are not virgin. Hundreds of years ago, most of its ancient trees were cut for lumber. The stumps remain everywhere, often uncorrupted and covered with moss or sprouting other trees, including second and third-generation cedar - Nidai and Sandai Sugi - in the continually regenerating forest. The remaining Japanese cedar trees over 1000 years old are termed yakusugi, and many revered trees have been given individual names. The largest, called the Jomon sugi, is estimated to be between 2100 years old (the oldest date that can be confirmed by carbon-dating of core samples) and 7200 years old (based on its size).
The pristine yakusugi forests were an inspiration for acclaimed animator Hayao Miyazaki's 1997 epic Princess Mononoke.
Because of the remoteness and difficulty of the terrain, there are relatively few tourists. Those who do come come to walk the forests. The well-trod hiking trails are entirely free of garbage. Visitors need to continue to ensure that no waste is left behind.
Human activity being a relatively small part of island life, there is abundant wildlife, notably a large deer and monkey population which goes about its life unconcerned by any humans in the vicinity. Wild monkeys should not, of course, be approached. Unlike some places where monkeys and humans interact, Yakushima monkeys are not fed by residents or tourists and so do not approach cars or persons for food. Don't feed the monkeys and this happy state of affairs will continue.
There are a few bilingual English/Japanese information signs on the hiking trails and in museums. As always the tourist information centers, particularly in Miyanoura, are extremely helpful although English may not be spoken.
The "Toppy" and "Rocket" Jetfoil ferries can be taken from Kagoshima; they both take approximately 2 hours depending on if there are stops at Ibusuki and Tanegashima. They cost 7100 yen (as of March 2011) and run 4 times a day, although regular ferry as well as jet foil ferry services are canceled in bad weather.
Ferries can arrive at either Miyanoura port or Anbo port, so take care to plan the following transport and accommodation accordingly.
Keep in mind this is a small island with few people. Relying on buses alone to get around can limit your ability to get places quickly. Private rentals are the way to go - rent a scooter if luggage allows as the one road around the entire island takes 3 hours to circumnavigate.
English is spoken less here than the cities, so bring a dictionary!
A highway runs around the island's coast. Buses travel most of this outer ring around once an hour from 07:00 to 18:00, taking in the airport, the two major ports, the beaches and hot springs.
Rental centers will rent out Cars, Scooters and Mountain Bikes for flexible periods of time from 3 hours to 2 days with built in extensions of a day - and penalties per hour late.
Electric Vehicles like the Toyota RAV4 EV can be seen (not heard) creeping around but sadly aren't for rent.
Taxis can be found at the airport and ferry ports around ferry arrival times - particularly the first arrival of the day - and are scarce at other hours.
From the Ferry Port
It's easy to feel a little lost when first getting off the ferry at Miyanoura port. There's just a few people, not many tourists to follow, no apparent guides to help you get on a bus, no taxi and within 15 minutes absolutely no people. Overall there are more vending machines than people walking on the street.
The ferry ports have separate landing wharves for the regular ferry, and the Toppy and Rocket companies. The regular ferry port contains some useful information pamphlets, including the complete Bus timetable with destinations in Kanji only.
Up the road out of the port (10 minute walk up the hill - take a left after you get out of one of the ferry lobbies) is the Environmental Centre and a cafe - Jane Bay Cafe last I checked. The Environmental Centre seems to be a touristy library pseudo museum but is also the equivalent to a Tourist Information Desk in Yakushima.
Do yourself a favour and cash up before coming in if possible. There's an ATM at the post office, which like all other Japanese Post Office ATMs accepts foreign cards. The closest one to Miyanoura port is a 30 minute walk up the road.
Most visitors come to experience the ancient cedar trees and forests. This requires some--or a lot of--hiking (see Do below).
There are several waterfalls on the island, including Ooko-no-taki which is justly rated as one of Japan's best. It is on the remoter southwest coast of the island, a 60- and 90-minute bus ride from Anbo and Miyanoura respectively. The 90-meter falls are easily accessible, being a short walk away from the main highway on a paved road, and visitors can approach the base for a good view. Those wanting to get closer and wetter can scramble over boulders to the plunge pool.
If you leave the towns, villages and main highway, you are almost guaranteed close encounters with the resident deer (shika) and monkeys (saru). Both varieties are small. If you have a car, the most accessible place to see them is the short section of coastal road in the west (south of Nagata) that has not been widened into a highway and where buses do not run. Here, deer often scramble down to the road, and in the afternoons monkeys groom each other on the warm asphalt, stopping all traffic.
On several beaches, including Nagata-inaka-hama Beach, giant turtles come ashore to lay their eggs. This is a rare occurrence from the end of May to August and very early in the morning (1AM-2AM). Only red flashlights may be used so as not to scare away the turtles (who are blind to red light). Two ecotour centers offer guided tours: Native Vision (Miyanoura), +81 (0)997 42-0091, . Outdoor Yakushima Guide System (Anbo), +81 (0)997 46-3220, . From ¥8000 per person.
You came to see the yakusugi cedar forests. There are three general areas to do this: the trail to and from where the Jomon sugi was, the Shiratani Unsuikyo (白谷雲水峡) forest, and the trails of Yakusugiland. Because of the (dubious) reputation of the oldest but deceased tree on the island, the Jomon sugi is the premier destination for most visitors. It can only be reached on foot, and to get there, hikers must be reasonably fit and start before dawn in order to complete the arduous 10 or 12-hour round trip. It is a beautiful and interesting enough hike, but the steep trail to and from Jomon sugi does not go through the most impressive forest on the island. To see the silent, mossy, primeval forest pictured in the tourist brochures, the better destination is the Shiratani Unsuikyo forest, and it doesn't require an early start and hours of tough hiking to get there.
The Shiratani Unsuikyo forest: This can be reached by car up the recently widened road, or by bus from Miyanoura (40 minutes; 530 yen). Admission to the trail is 300 yen, to cover maintenance. A map and suggested routes based on your time constraints are provided at the trail head. There are two main hiking options: a 3 to 4-hour route through an awe-inspiring forest with a half-dozen or so yakusugi and more moss than you can shake a stick at; and a 30-minute there-and-back hike to the magnificent 3000-year-old cedar called Yayoi sugi. The longer route begins with a series of wooden steps and walkways past waterfalls. A loop to the right takes in the Yayoi sugi but it's recommended to leave this until last. Keep going ahead for 15 minutes until you come to a suspension bridge. Don't cross the bridge but walk ahead into the forest proper where the trail climbs past mossy stumps and ancient trees, and drops down to boulder-strewn drinking streams, leading you deep into another silent world. Deer and monkeys graze and feed unafraid. After about two hours of walking with stops to take in the natural marvels of the forest, the trail divides, with an option to turn right to Shiratani hut and Mononoke-hime no Mori, a part of the forest named after Hayao Miyazaki's anime movie Princess Mononoke. You miss nothing by turning left here and heading back via the original Edo-period Kusugawa trail. After an hour's walk, it ends in the trail's old granite steps down to the suspension bridge. Cross the bridge, turn right, take the loop up to the left to Yayoi sugi if you still have the energy, and return down to the trailhead. This hike is not especially arduous, and is arguably the most beautiful on the island.
Yakusugiland: In spite of its theme-park name, this is another natural area for walking in the forest among yakusugi, with a variety of hiking options based on time (there are 30, 50, 80 and 150 minute round trip trails). It is less accessible than Shiratani Unsuikyo, being further from the coast with a narrower access road and fewer buses.
To and from Jomon sugi: The usual way to approach the remains of the giant tree is via the Arakawa trail, a round trip of approximately 10 hours. There is limited parking at the trail head, or it can be reached by a complex series of buses. First, drive, or take a bus or taxi to the Yakusugi Museum (Yakusugi Shizenkan) Complex. The trip from here to the trail head at Arakawa Tozanguchi bus stop is on two further buses with the change halfway and a combined fare of 1010 yen. The first, easy part of the hike is along the tracks of the railroad used to haul out cedar logs. After about two hours, the trail turns off the rails and from here it's a hard two-hour climb up the well-maintained path, passing Wilson's Stump, the huge hollow remains of a logged tree, and on up to Jomon sugi itself. Many visitors make the hike in a group with a guide. This isn't necessary as the trail is well-marked, but a guide enriches the experience by pointing out and giving you the (Japanese-language) inside information on the history and landmarks. Food and water must be carried in, but water can be replenished halfway along the railroad and at the drinking streams near the destination. Solid walking shoes or light hiking boots are best, with sneakers possible if you're careful. It rains at least part of most days, so pack an umbrella or plastic rain jacket. Because of the hiking time and time required to get to the trails from the coast, hikers often start out before 5 am. If you have not reached the remains of the Jomon sugi by 1 pm, it may be advisable to turn around or you may by caught on the trail by night fall. An alternative way to Jomon sugi is starting at Shiratani Unsuikyo. This route begins with the hike through the Shiratani Unsuikyo forest (see above), taking the right fork to Mononoke-hime-no-Mori, then climbing steeply toward (but not to) Taikoiwa rock, and going over the Tsujitoge pass before descending to join the Arakawa trail where it turns off the railroad, for a 12-hour round trip.
Longer hikes with overnight stays are available for the adventurous. The hiking trails are among the most pristine and lonely in Japan. The hike to the top of the highest peaks Miyanoura-dake (1867 meters) and Nagata-dake (1886 meters) and back (or across the island) is tough, typically requiring two to four days depending on the route you select. There are a few mountain huts along the way, but they are nothing more than empty structures so bring your own bedding and provisions. It will rain.
There are a few white sand beaches with clear water at various places on the coast. If there is no lifeguard, swim with caution. Nagata-no-hama beach has a small reef system nearby so it is possible to see some marine life. At the southern/western end of this beach there are some showers available for use.
Scuba is also available.
Seaside onsen can be enjoyed at Kaichuu onsen（海中温泉) in Hirauchi（平内), and a few kilometers west at Yudomari onsen below picturesque Yudomari village. Both have 100 yen entrance fees, placed in a trust box. Kaichuu onsen is only available for a few hours before and after low tide. It is also very well-known, and the constant flow of visitors can make it a less-than-relaxing place to bathe. Far better is Yudomari onsen (open 24 hours). The tiny main pool has a bamboo screen that offers a modicum of separation between the sexes. But keep walking down the concrete path to the left of this bath and you will come to an even smaller, more private pool. Between soaks, slip down to the sea for a swim among the rocks. Just outside the entrance to Yudomari onsen, a small bar serves cold beer and other drinks and snacks.
Using the local cedar, artisans craft a great variety of goods such as chopsticks and sake cups in all price ranges for the souvenir trade.
Local specialties include flying fish and two varieties of orange: tankan and ponkan.
On the coast road south of Anbo, by the parking lot for Toroki Falls, a produce center sells fruit in season and other local goods and produce including tankan juice, ice cream and sherbet. (The Toroki Falls are a 5-minute hike away. They fall directly into the sea, but are underwhelming.)
The local shochu is worth sampling. The most famous is called Mitake, and comes in a 25 percent and 32 percent variety.
Cottage Morinokokage is log cabin cottages in Funayuki. There are 9 individual log cabins, and 3 different types of room are available. Amenities are TV, air-conditioner, refrigerator, electric pot, dryer, Japanese Tea Set,candle lantern, bath & shower (inc. shampoo, hair conditioner, body soap, and hand wash soap), toilet, mexican hammock, garden table, swing, low rebound mattress & pillow, free parking space, laundromat in property, and smoke free in the room.
It is located between Anbo and Miyanoura, where easy access to main sightseeing spot such as Jomonsugi and Shiratani Unsuikyo. Only 5 mins drive from Anbo port, 8 mins drive from Yakushima air port, and 20mins drive from Miyanoura port.
There is excellent mountain(Myoujou-dake & Funayuki-maedake) view from each rooms, and shining star can be seen at night. Walking distance to seashore to see beautiful sunrise and Tanegashima island. Breakfast, BBQ, early Bento delivery, local restaurant, taxi, rental car can be arranged.
Camping is not allowed in the national park, but backpackers can find several small huts along the trails in the central mountains of the island that they can stay in free of charge. These huts vary in size and can accommodate anywhere from 20-60 people. However, they are little more than four concrete or wooden walls and a roof, and at night they get very cold. Backpackers should be well equipped with sleeping bags and heavy clothing even when weather along the coast is warm and pleasant. Rental equipment from Miyanoura is not always up to par. Camping sites at the coast are about ¥800 and a few backpackers starting from ¥1600 for accommodation only.
There are three budget type accommodations on the island, which offer dormitories and privates starting at about ¥3000 per person.
There are many small lodges which run 5000-8000 yen with 2 meals.
Shiki no Yado Onoaida (四季の宿 尾之間)  in Onoaida (尾之間) is a small family run lodge with a choice of Japanese style rooms, Western rooms or cottages. The price is around 8000 yen per person, per night including breakfast and dinner.
Lodge Yaedake Sanso （ロッジ八重岳山荘）, off the track from 牛床公園 bus stop on the route up the mountain from Miyanoura to Shiratani Unsuikyo, is a ryokan (separate toilet and hot spring water bath) with tatami mat rooms interconnected with wooden walkways. It is located within a forest of thin cedar trees which the rooms have balconies opening onto, and is right next to a clean, fresh water river. There are kayaks, a barbecue area, and a free laundry and dryer.
During the rain it is a cosy, lovely, dark, and aromatic experience in sharp contrast to the dense compact cities of modern Japan.
As per Shiki no Yado it's around 7-8,000 yen a person a night, including dinner and breakfast. Beer is separately purchasable, and for an extra 6-700 yen they will pack you a bento for lunch the next day - this is recommended as it can be hard to find a restaurant or food for sale on the hiking trails.
As it's quite out of the way, pick up at 4PM at the Minshuku run by the same people near Miyanoura (Minshuku Yaedake Honkan 民宿八重岳本館) can be arranged during the booking or rock up and ask for the pickup
JR Hotel Yakushima  in Onoaida has twin rooms from 15,000 yen per person per night including breakfast and dinner. The modern nonagonal hotel building is situated on a point so the Pacific horizon seems to stretch endlessly. Opposite, the island's mountains rise in a sheer rock face. The rooms and food are excellent, and there is a hot spring (including rotenburo outdoor pool) overlooking the ocean. But what most impresses is the polite and thoughtful staff and service, impeccable even by Japanese standards.
Some snakes. The coastline is beautiful, but rough; bathing in the wrong place might be dangerous.