Class I

Union Pacific (UP)

BNSF

Class III

California Northern Railroad (CFNR)
Central Oregon & Pacific Railroad (CORP)
San Diego & Arizona Eastern Railway (SDAE)
San Diego & Imperial Valley Railroad (SDIY)
Central California Traction (CCT)
Los Angeles Junction Railway (LAJ)
Mendocino Railway 
Modesto & Empire Traction (MET)
Oakland Terminal Railway (OTR)
Pacific Harbor Line (PHL)
Pacific Sun Railroad (PSRR)
Quincy Railroad (QRR)
Richmond Pacific Railroad (RPRC)
Sacramento Valley Railroad (SAV)
Santa Cruz, Big Trees & Pacific Railway (SCBG)
Santa Maria Valley Railroad (SMV)
San Joaquin Valley Railroad (SJVR)
Sierra Northern Railway (SERA)
Stockton Terminal & Eastern Railroad (STE)
Trona Railway (TRC)
Tulare Valley Railroad (TVRR)
Ventura County Railroad (VCRR)
West Isle Line (WFS)
Yreka Western Railroad (YW) 

Commuter Rail

Altamont Commuter Express (ACEX)
Amtrak (ATK)
Caltrain (PCJX)
Metrolink (SCAX)
North County Transit District Coaster (NCTD)

California High-Speed Rail

California HSR Authority

CPUC regulates all railroads in California. The above list does not limit the jurisdiction of CPUC regulation.