Ismael Zambada Garcia, known as "El Mayo," co-founder of the cartel, and Joaquin Guzman Lopez, a son of its other co-founder, were taken into custody in El Paso, Texas, on Thursday, US officials said.
Biden described the pair as "two of the most notorious leaders of the Sinaloa Cartel" and said US authorities "will continue doing everything we can to hold deadly drug traffickers to account and to save American lives."
"Too many of our citizens have lost their lives to the scourge of fentanyl," he said.
Attorney General Merrick Garland, who announced the arrests late Thursday, said the 76-year-old Zambada and Guzman Lopez, who is in his mid- to late 30s, would appear in federal court in the coming days.
Zambada faces charges for fentanyl trafficking, money laundering, firearms offenses, kidnapping and conspiracy to commit murder, he said, while Guzman Lopez is charged with trafficking cocaine, heroin and meth and other drugs.
Mexico said Friday it played no part in the arrests, seen as a major blow to the Sinaloa Cartel.
"The government of Mexico did not take part in this arrest or surrender," state security director Rosa Icela Rodriquez said.
President Andres Manuel Lopez Obrador said he expected a "complete report" from the United States on how the men were taken into custody. "There must be transparency," he told a news conference.
Garland did not release details about the arrests but US media quoted law enforcement sources as saying they were the result of a sting operation in which Zambada was unwittingly lured across the border by Guzman Lopez.
Guzman Lopez's father, Sinaloa Cartel co-founder Joaquin "El Chapo" Guzman, was convicted of drug charges in New York in 2019 and is serving a life sentence in a maximum security prison.
Guzman Lopez is one of El Chapo's four sons known as Los Chapitos, or "The Little Chapos." One son, Ovidio Guzman Lopez, was arrested in Mexico in 2023 and extradited to the United States.
According to a US Drug Enforcement Administration (DEA) report released in May, Los Chapitos were engaged in an internal battle against Zambada, their father's former partner.
CNN, citing a US law enforcement official, said the US authorities exploited the "rift" in the cartel to capture Zambada.
The official said Zambada boarded a plane with Guzman Lopez for a flight that he believed was intended to inspect property in Mexico near the US border. Instead, the plane landed in the Texas border town of El Paso where both men were arrested.
The Wall Street Journal said the operation had been in the works for months.
NBC News said Guzman may have decided to surrender and was "under the impression he would receive more favourable treatment if he brought with him another major cartel figure."
DEA chief Anne Milgram said Zambada's arrest "strikes at the heart of the cartel that is responsible for the majority of drugs, including fentanyl and methamphetamine, killing Americans from coast to coast."
And the capture of El Chapo's son marks "another enormous blow to the Sinaloa Cartel," Milgram said.
The low-profile Zambada, who has never served time in prison, cultivated close connections over the decades with Mexico's federal police and military and has been wanted in the United States for decades.
His son, Vicente Zambada Niebla, was arrested by the Mexican authorities in 2013 and extradited to the United States.
Zambada Niebla testified against 'El Chapo' at his 2019 trial and revealed details of the cartel's smuggling operations, claiming his father had a "bribery budget" of US$1 million per month, much of it going to high-level Mexican public officials.
The US State Department had offered a reward of US$15 million for the arrest of Zambada and US$5 million for the capture of Guzman Lopez.
Victims of the cartels' ultra-violent turf wars include rival gang members, security personnel and journalists, among more than 450,000 people murdered since the government launched a military offensive against drug cartels in 2006.
The United States saw more than 107,000 drug overdose deaths in 2023, according to the Centres for Disease Control and Prevention. Fentanyl accounted for about 70 percent of them.
--TIMES/AFP
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