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Founded in 1912, the San Francisco Municipal Railway (Muni) is one of America's oldest public transit agencies, and today, it carries over 200 million riders per year. Muni provides transit service within the city and county of San Francisco 24 hours a day, 7 days a week. Operating historic streetcars, modern light rail vehicles, diesel buses, alternative fuel vehicles, electric trolley coaches, and the world-famous cable cars, Muni's fleet is among the most diverse in the world.

Sonoma-Marin Area Rail Transit (SMART) is the Bay Area’s newest passenger rail service, providing a safe, reliable, and congestion-free transportation option for Marin and Sonoma counties. The 45-mile system includes stations in the Sonoma County Airport area, Santa Rosa, Rohnert Park, Cotati, Petaluma, Novato, San Rafael, and Larkspur. Future extensions are planned for Windsor, Healdsburg, and Cloverdale, completing the vision for a full 70-mile system.

SolTrans provides local and express bus service to the Solano County cities of Vallejo, Benicia, and Fairfield, and Suisun City with express bus service connecting to the Contra Costa County communities of El Cerrito, Pleasant Hill and Walnut Creek at BART stations. Nine local fixed routes serve Vallejo, five limited service routes operate during school in-service dates within Vallejo and Benicia, and two express routes connect Benicia and Vallejo to surrounding areas.

Sonoma County Transit provides intercity bus service in Sonoma County and local service in Rohnert Park, Cotati, Guerneville, Sebastopol, Sonoma, and Windsor.

The South City Shuttle is a free shuttle service in South San Francisco. The shuttles operate Monday through Friday, offering free service throughout the City, with stops at local stores, senior centers, libraries, City Hall, and parks. The shuttle also provides transit connections with SamTrans and BART.