In a letter, translated in English and read by his lawyer, Arellano Felix asked people on both sides of the border to forgive his "wrongful decisions and criminal conduct."
"I am very remorseful and personally accept responsibility for my actions," he wrote. "If I had the power to change and undo the things that I have done, I would."
Arellano Felix, 37, was captured after a manhunt by U.S. authorities in an August 2006 raid on a sportfishing yacht off the Baja California coast. At his arraignment after the arrest, he appeared wearing a plain orange T-shirt, designer plaid shorts and flip-flops; at his sentencing, he wore a standard-issue orange prison jumpsuit.
Arellano Felix, the youngest of the cartel's seven brothers, pleaded guilty Sept. 7 to running a criminal enterprise and conspiring to launder money. Those crimes carry a mandatory life sentence.
"I tell you today, man to man, that even if I had the discretion not to impose a life sentence in this case, that's what I'd find most reasonable," U.S. District Judge Larry A. Burns said.
The judge, who earlier in the day heard a handful of the drug-smuggling cases that routinely clog his courtroom, minced no words in admonishing Arellano Felix for his role in encouraging drug use.
"Your family's name will live in infamy," Burns said. "The effect on this country of what you and your family have done is disastrous."
Arellano Felix, who has been in custody without bond at a downtown San Diego federal detention facility, is not currently eligible for any kind of parole, Burns said.
His lawyer, David Bartick, said after the sentencing that Arellano Felix was prepared to be sent to the so-called Supermax prison in Florence, Colorado, where America's most violent criminals are held. A final decision on where Arellano Felix will be housed rests with the federal Bureau of Prisons.
The Arellano Felix cartel emerged as a drug trafficking powerhouse in the 1980s in Tijuana, across the border from San Diego, though its influence is widely believed to have waned in recent years as its leaders have been killed or captured.
The cartel was once led by seven brothers and four sisters, but Francisco Javier's brother Ramon was killed in a shootout with police in 2002. His elder brother Benjamin was jailed in Mexico the same year; federal prosecutors in San Diego are seeking his extradition to face charges in the United States.
Prosecutor Laura Duffy said she does not know when Benjamin Arellano Felix will be extradited, but said she hoped it would be soon.
"I thought he'd be here by now," she said after the sentencing. She said she was pleased to have extracted a plea from Francisco Javier because it allowed the government to keep its evidence secret ahead of any proceedings against his older brother.
Arellano Felix was captured during a U.S. Coast Guard-led raid off La Paz, Mexico, and towed back to San Diego aboard his 43-foot yacht, the Dock Holiday. The arrest at sea came after an intense manhunt, during which the State Department had offered a $5 million reward for the drug lord's capture.
Also aboard the boat was Arellano Felix's right-hand man, Manuel Arturo Villarreal Heredia, who pleaded guilty to racketeering and conspiracy to invest illicit drug profits. He faces up to 30 years in prison when he is sentenced in January.
Since their capture, Arellano Felix's older brother Francisco Rafael and two senior cartel capos have been extradited to the United States and sentenced on drug charges in San Diego.
Arellano Felix admitted in court that he helped run the cartel as it brought into the United States hundreds of tons of cocaine and hundreds of tons of marijuana and laundered hundreds of millions of dollars.
According to his plea agreement, Arellano Felix and his partners murdered informants and potential witnesses and paid millions of dollars in bribes to law enforcement and military personnel.
He agreed to forfeit $50 million and the yacht Dock Holiday.