The arrested man was used car salesman Felix Beltran Leon, not Jesus Alfredo Guzman, whose father heads the powerful Sinaloa drug cartel, the BBC reported Friday.
The British broadcaster said doubts arose hours after Beltran Leon was shown off to the media Thursday.
In a statement, a lawyer saying he was a spokesman for the Guzman family denied that the man in custody was the drug lord's son.
Beltran Leon's mother talked to reporters and denied any ties between her son and Joaquin Guzman or the Sinaloa cartel.
Identity tests were performed then the government admitted it had made the mistake.
Known as El Chapo," or "Shorty", Joaquin Guzman has been in hiding since he escaped from prison in 2001. The Sinaloa cartel directs much of the distribution of cocaine, marijuana and methamphetamine to the United States.
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