The 14-year-old, called El Ponchis, claims he carried out at least four executions for Mexican drug traffickers.
Border Patrol agents arrested Yolanda Lugo Jimenez, 43, on Monday night at her San Diego home, according to a federal complaint filed Wednesday. Jimenez allegedly told agents she is a Mexican citizen and not allowed to be in the United States.
A U.S. Embassy spokesman said on Tuesday that consular officials had not yet determined the boy's citizenship. Spokesman Alexander Featherstone said officials visited the boy Monday to provide him with information on a local attorney and to monitor his welfare.
Featherstone said Tuesday that the embassy has not confirmed his citizenship but that he was offered consular assistance "in case he is a U.S. citizen."
Mexican officials and the boy's family say he was born in the United States.
Meanwhile, Mexican prosecutors said they are detaining two of the boy's sisters for 30 days for investigation of possible kidnapping charges. The women are aged 19 and 23. The boy is being held at an undisclosed location to protect his safety.
The boy reportedly told Mexican investigators last week that he had been working for the cartel since he was 11.
The much-rumored alleged young assassin was captured late Thursday as he tried to catch a flight to Tijuana with his sister and flee the country, said an official, who requested anonymity because he was not authorized to discuss the case.
The sister told reporters that they planned to cross the border to San Diego, where their mother lives.
The two were brought to the office of the Mexican Attorney General's Office in Cuernavaca early Friday, where the boy told reporters he had participated in at least four decapitations. The source said his sister was accused of getting rid of the bodies by dumping them on streets and freeways.
"I participated in four executions, but I did it drugged and under threat that if I didn't, they would kill me," said the teen, who appeared calm and showed no remorse.
Another teenage sister accompanied the two, but officials said she was not suspected of being involved in the cartels.
During the news conference, the boy wore the blue jeans and a T-shirt he was wearing when he was taken into custody. The army did not specify where they were detained in the airport or whether they had already passed through security checks.
The brother and sister are suspected of helping the South Pacific Cartel headed by Hector Beltran Leyva, brother of Arturo Beltran Leyva, a top drug lord who was killed by Mexican marines in Cuernavaca a year ago. Hector Beltran Leyva's fight for control of the cartel has caused a major spike in violence in the state just south of Mexico City, and in neighboring Guerrero state, where the resort of Acapulco is located.
The siblings were living in a poor neighborhood of Jiutepec, a working-class suburb of Cuernavaca, known as a weekend getaway for Mexico City residents. The area has an industrial area with Nissan, Unilever and other factories, rustic single-level concrete homes and some farms.