Omar Mateen pledged allegiance to the Islamic State group during the standoff at Pulse Nightclub on June 12, when 49 people were killed and dozens more were injured.
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Salman is also charged with obstruction of justice.
"(Salman) did knowingly engage in misleading conduct ... with the intent to hinder, delay and prevent the communication to federal law enforcement officers and judges of the United States of information relating to the commission and possible commission of a federal offense," the indictment said.
The FBI arrested Salman Monday just after 8 a.m. local time at a home in Dublin, California, her booking listing at the Santa Rita Jail in Alameda County said.
>> FBI arrests wife of Pulse nightclub shooter
Some neighbors said they were not surprised.
"I kind of thought since she's living that close to somebody and married to him that she may have known more than she's putting out," said neighbor Catherine Lawrence. "(I'm) not surprised after kind of hearing all about it."
Salman's former special education teacher, who asked not to be identified, came to the woman's defense, saying she didn't have the mental capacity to comprehending what was happening.
"I thought, 'She is incapable of being an accomplice, absolutely incapable,'" the teacher said.
Salman is charged with obstruction of justice and aiding and abetting the attempted provision of material support to a foreign terrorist organization.
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