If you want a bargain for transportation, it's best to go by train or bus. We booked our tour through a travel agency, and the agent recommended going down by bus and coming back by train. Why? You can ride the bus through the night and end up straight at Surat Thani, the departure point for ferries to the islands. If you want to go by train, you have to get off at the station and then take a bus to the pier. Taking the overnight train on the return trip, you go straight into Bangkok without extra stops (and can sleep most of the way).
Boats from Surat Thani usually arrive at the Na Thon pier on Koh Samui, the island's transportation hub. This is on the western coast of the island, opposite from Hat Chaweng or Hat Lamai - Koh Samui's most popular beaches - on the east. ("Hat" is Thai for beach.) While you wait in Surat Thani for your boat, you can arrange for a minibus to take you to your beach, but you'd probably save money with a cab - it was 100 baht per person for the minibus, whereas with a cab you could split higher fares between three to four people. Or save even more money and look for a songthaew, a truck with benches in back. The fare to Hat Chaweng or Hat Lamai is 40 baht, but because it stops for anyone who needs a ride, it can take a long time to get to the other side of the island.
You can also fly into Koh Samui at the Samui Airport. The airport is between Hat Chaweng and Big Buddha Beach on the northeastern tip of the island. A flight from Bangkok is 3450 baht, and it's 1820 baht from Phuket. There's a 400 baht departure tax for domestic and international flights.
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