The FBI on Monday arrested the wife of the gunman in the Pulse Nightclub massacre on charges connected to the shooting rampage, investigators confirmed to Fox News.

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The June 2016 shooting, seen as the deadliest in modern U.S. history, killed 49 people and wounded dozens more. Police shot and killed gunman Omar Mateen after a three-hour standoff, during which he pledged allegiance to the Islamic State terror group.

The charges against his wife, 30-year-old Noor Salman, included aiding and abetting his attempts to support ISIS, as well as obstruction of justice.

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According to a source close to the investigation, the U.S. Attorney in Florida and attorneys within the Dept. of Justice, the agencies, which jointly prosecute terrorism cases, wanted to charge Salman with directly supporting ISIS, in addition to aiding the terror network through her husband. However, Acting Assistant Attorney General Mary McCord refused to support additional charges.

FBI agents from the bureau's San Francisco field office picked up Salman outside her home in Rodeo, Calif., law enforcement sources said. She did not resist the arrest.

In April 2016, Mateen and Salman took their 3-year-old son to Walt Disney World, but their behavior reportedly was alarming enough for Disney officials to have contacted the FBI to alert them that Mateen and Salman appeared to be scouting the theme park as a venue for a potential attack. The family went to another Disney property, Disney Springs, that June.

During the attack that began around 2:00 a.m. on June 12, Mateen placed 16 calls, an FBI source told FoxNews.com, and communicated by SMS, a texting service.

At least three calls were to 911 and one was to a local news service, during which he pledged his allegiance to ISIS and expressed support for the Boston Marathon bombers, Tamerlan and Dzhokhar Tsarnaev.

He texted Salman during his shooting rampage, made posts to his Facebook account proclaiming his allegiance to ISIS and pledging more attacks, and according to an FBI source, used the social media platform Snapchat to communicate with at least one other person.

Salman is set to make her initial appearance in federal court Tuesday in San Francisco. She had moved to Contra Costa County after the shooting.

The charges were filed in the Middle District of Florida - the jurisdiction in which the nightclub massacre took place. Following her initial appearance, the plan is to fly Salman back to the Middle District of Florida where she will continue through the judicial process.

The New York Times first reported Monday's arrest.

Salman claimed last November she had no clue about what her husband was planning, according to a Times interview. "I was unaware of everything."

She also said Mateen got increasingly violent as their marriage got rockier, even punching her in a fit of rage while she was pregnant, during a trip to buy baby clothes.

Her son, now 4, is partly named for his father. Salman filed a petition to change the boy's name last month.

The Justice Dept. released transcripts of Mateen's 911 calls after the shooting. In one call, he said, "Praise be to God, and prayers as well as peace be upon the prophet of God [in Arabic]. I let you know, I’m in Orlando and I did the shootings."

"Nothing can erase the pain we all feel about the senseless and brutal murders of 49 of our neighbors, friends, family members and loved ones. But today, there is some relief in knowing that someone will be held accountable for that horrific crime," Orlando Police Chief John Mina responded.

One of the officers who responded to the massacre, Master Sgt. Debra Clayton, was shot and killed last week outside a Walmart in the city. Her suspected killer, Markeith Loyd, remained on the loose one week later.

FoxNews.com's Malia Zimmerman, Fox News' Mike Lundin in Rodeo, Matt Dean, Jennifer Griffin and The Associated Press contributed to this report.