In a rare but not surprising move, a federal judge in Brooklyn has ruled that when Joaquín Guzmán Loera, the Mexican drug lord known as El Chapo, goes on trial in September, the case will be heard by an anonymous and partly sequestered jury.

In an order issued Monday night, the judge, Brian M. Cogan, said that Mr. Guzmán’s “history of violence” warranted keeping secret the jurors’ names, work places and addresses throughout what is likely to be a three- or four-month trial. Judge Cogan also ruled that the jurors should be driven to and from their homes to Federal District Court in Brooklyn by armed federal marshals. He added that he will tell the jurors the restrictions were being put in place “to protect their privacy and to ensure that the trial proceeds expeditiously.”

The use of anonymous juries has long been controversial because it can erode the presumption of innocence and prejudice jurors against a defendant before they have a chance to consider any evidence. Although Mr. Guzmán, the reputed former leader of the Sinaloa drug cartel, has not been charged directly with any violent crimes, the government has claimed, in public documents and several secret filings, that he once maintained an army of assassins who carried out hundreds of murders, assaults and kidnappings on his behalf — some of them to silence potential witnesses, others to take revenge against those who had betrayed him.