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Below is a link for the Costa Rica Tourist Board site that has the most updated bus schedules for all of Costa Rica:
http://www.visitcostarica.com/ict/paginas/LEYES/pdf/ItinerarioBuses_en.pdf

It is highly advisable to purchase bus tickets at least one day in advance for long trips unless you don't mind standing in the aisle!

Travel by bus from San Jose to San Vito: (times updated 12/27/08)
(see map below for bus terminal locations; click for a larger view)
You can take a Tracopa Ltda Zona Sur bus from the new terminal in Zapote (near Parque Viquez on the southeast side of the city, between Avenidas 18 and 20 and Calle 5, just one block north of the large, yellow-walled MOPT building); it will go through San Isidro, Buenos Aires, Paso Real en route to San Vito.

Tracopa buses now leave the new Tracopa terminal at 6:00 am, 8:15 am, 12:00 noon (Directo), and 4:00 pm. Buses return from San Vito to San José at 4:00 am (Directo), 6:30 am, 9:00 am, and 2:00 pm. Tel: (San José) 2221-4214, (San Vito) 2771-0468.*

Travel by bus from San Jose to San Isidro: (check the times as they may have changed)
A Musoc bus, route 100 or 100SD, from the new Musoc terminal at C-Central/A22-A24, leaving at 5:30 am, 7:30 am, 10:30 am, 11:30 am, 1:30 pm, 2:30 pm, 4:30 pm, and 5:00 pm; duration 3 hours, regular or direct service ˘ ˘1,600. Buses return to San José at 5:00 am, 5:30 am, 7:30 am, 8:30 am, 10:30 am, 11:30 am, 1:30 pm, and 4:30 pm. Tel: (San José) 2222-2422 or 2223-0686, (San Isidro) 2771-0414 or 2771-3829. Buy your ticket in advance Mondays through Fridays. Tickets are not sold on Saturdays or Sundays. Arrive at least 30 minutes before departure or your seat may be resold.

Or, take an Empresa Gafeso bus, route 100 or 100SD, leaving from C16/A1-A3 across the street from Coca Cola at 6:30 am, 8:30 am, 9:30 am, 12:30 pm, and 3:30 pm, duration 3 hours, regular or direct service ˘1,600. Buses return at 6:30 am, 9:30 am, 12:30 pm, 2:30 pm, and 3:30 pm. Tel: (San José) 2222-9763, (San Isidro) 2771-2550.

You can take any of the regular service Tracopa Ltda Zona Sur buses from the new terminal in Zapote (near Parque Viquez on the southeast side of the city, between Avenidas 18 and 20 and Calle 5, just one block north of the large, yellow-walled MOPT building), to Palmar Norte, Golfito, Ciudad Neily, San Vito, or Coto 47. Get off at San Isidro de El General. Tel: (San José) 2222-2666, 2255-4827, or Fax: 2255-2981. However, tickets are not sold for Zona Sur buses returning to San José. You can pay on the bus if there is space available, but you may not have a seat.

Tip:   Buses from San José to San Isidro de El General travel via the Carretera Internacional over the Talamanca mountain range, climbing to an altitude of 10,000 feet (3,040 meters) at Cierre del Muerte (the "Mountain of Death"), where travelers once camped overnight and died of exposure. The views are spectacular. Bring a waterproof jacket and one or more sweaters. From San Isidro, you can return to San José via the Costanera, which follows the Pacific coastline, passing through numerous beachfront communities. Take the Dominical or Quepos bus from the Transportes Blanco station off Avenida 2 in San Isidro on the last street to the right before A2 intersects the Carretera Interamericana. You can see the mountains, then "beach hop" back to your point of departure.*

  *(portions of above were taken from http://www.costaricabybus.com/ctytown.html)

Click map for larger view.