The FBI said a recent tip led agents to an apartment in the 1000 block of Third Street where 81-year-old Bulger and his longtime girlfriend, 60-year-old Catherine Greig, were living.
Bulger was on the FBI's "Ten Most Wanted" list for his alleged role in 19 murders, among other crimes.
He is known as the leader of the Winter Hill Gang, a largely Irish mob that ran loan-sharking, gambling and drug rackets in the Boston area.
Bulger has been the subject of several books and was an inspiration for the 2006 Martin Scorsese film "The Departed."
He fled Jan. 1995 after being tipped by a former Boston FBI agent that he was about to be indicted. That FBI agent, John Connolly Jr., had made Bulger an FBI informant 20 years earlier. Connolly was convicted of racketeering in May 2002 for protecting Bulger and his cohort, Stephen "The Rifleman" Flemmi, also an FBI informant.
On Monday, the FBI announced a new publicity campaign and accompanying public service ad that asked people, particularly women, to be on the lookout for Bulger's girlfriend. The 30-second ad started running Tuesday in 14 television markets.
Bulger faces a series of federal charges including murder, conspiracy to commit murder, narcotics distribution, extortion and money laundering.
Both were arrested without incident and are scheduled for a court appearance in downtown Los Angeles on Thursday.
The Associated Press contributed to this story