The Mexican government says Gildardo Lopez Astudillo, known as “El Gil” is a leader of the Guerreros Unidos drug cartel.
It alleges Gildardo Lopez Astudillo, 36, gave the orders to abduct and kill the students.
There have so far been 111 arrests over the 2014 disappearances.
The Mexican attorney-general’s office says its investigations show the Guerreros Unidos gang were handed the students by corrupt police in Iguala.
The office has said because Guerreros Unidos thought the students were members of a rival gang, they murdered them and then disposed of the bodies by burning them at a rubbish dump outside the city.
Official accounts contrast with a report issued by an international group of experts appointed by the Inter-American Human Rights Commission (IAHRC).
Their report earlier this month alleges that the Mexican authority’s investigations were deeply flawed, and included the disappearance of key evidence.
According to the experts, who visited the site where the Mexican authorities say the bodies were burnt, a fire fierce enough to incinerate the 43 students would have lasted over 60 hours and would have required tons of wood or rubber which would have burnt down the surrounding vegetation.
No fire was reported in the area at the time of the disappearance.
Earlier this week Austrian forensic experts announced they had identified the remains of a second victim found at the rubbish dump where the students’ bodies were allegedly burnt.
The relatives of the 43 students have demanded that the government investigates the possible involvement of high-ranking members of the military in the disappearances.
The apparent massacre of poor, rural students has posed problems for President Enrique Pena Nieto who took office in 2012 promising to stamp out drug-related violence.
Enrique Pena Nieto has been criticized for his handling of the case and accused of trying to wrap it up without a comprehensive investigation.
Correspondents say by charging “El Gil” with the disappearance of the students, the President would enable a swift end to the investigation.
International experts have disputed the government’s accounts of what happened and have said its investigation was deeply flawed.
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