There are several public transportation systems that operate in San Francisco, with many extending into other Bay Area counties.
The San Francisco Municipal Transportation Agency, often referred to as "SF Muni" or simply "Muni", is the city government department that manages the bus, streetcar and cable car lines operating within the city limits. The agency also manages automobile parking permits, parking meters and parking fines within San Francisco. The SFMTA website is http://www.sfmta.org
The Bay Area Rapid Transit System, commonly known as BART, is a system of heavy-rail electric trains that connects San Francisco with Alameda, Contra Costa and San Mateo counties. The BART website is http://www.bart.gov
The Golden Gate Bridge Highway and Transportation District is the agency that manages bus lines and ferry routes between San Francisco and Marin County, as well as matters related to the Golden Gate Bridge. Their website is http://goldengatetransit.org
samTrans is the San Mateo County public transit agency. San Mateo county is immediately south of San Francisco and comprises the majority of what locals refer to as "The Peninsula". SamTrans busses make stops in several locations within San Francisco. The samTrans website is http://www.samtrans.com
Caltrain is a commuter rail line connecting San Francisco with locations in San Mateo and Santa Clara counties. Their website is http://www.caltrain.com/