Juan Thompson, 31, was arrested in St. Louis and will appear in federal court in Missouri on Friday afternoon on a charge of cyberstalking, authorities said.
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Investigators are working to determine the suspect's role in recent other threats against Jewish organizations across the country since January. The complaint uses the term "JCC threats" to also include wider incidents involving Jewish schools and institutions.
Thompson is accused in what federal prosecutors called a "campaign to harass and intimidate." He's charged in New York with cyberstalking a woman by communicating threats to JCCs in the woman's name. Prosecutors said Thompson "appears to have made at least eight of the JCC threats as part of a sustained campaign to harass and intimidate" the woman after their romantic relationship ended.
According to a federal complaint, Thompson dated the woman until last summer, when they broke up. The following day, her boss received an email purporting to be from a national news organization saying that she'd been pulled over for drunken driving.
The harassment got worse from there, federal officials said. The Anti-Defamation League received an email on Feb. 21 that said she was behind the bomb threats to JCCs and there'd be more the next day. On Feb. 22, it received a phoned-in bomb threat.
He also claimed she was responsible for placing a bomb in a Jewish center in Dallas, and he emailed a JCC in San Diego saying she wanted to "kill as many Jews asap."
The eight threats include:
Feb. 21 - ADL email threat
Feb. 22 - ADL phone threat
Feb. 21 - Council of American Islamic Relations emails threat, "bomb in the jewish center in dallas"
Feb. 20 - JCC in San Diego, email threat
Jan. 28 - Jewish History Museum in Manhattan, received bomb threat
Feb. 1 - Jewish school in Farmington Hills, Mich., received a bomb threat
Feb. 1 - Jewish school in Manhattan, two separate bomb threats of "a Jewish newtown"
Feb. 7 - JCC in Manhattan, received a bomb threat
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Thompson is also a former journalist who was fired from the Intercept last year after he was accused of fabricating several quotes and creating fake email accounts to impersonate people, one of whom was the Intercept's editor-in-chief, Betsy Reed. One of the stories involved Dylann Roof, the Charleston, South Carolina, church shooter.
The ADL said Friday that Thompson had been on its radar ever since he fabricated the story about Roof.
Federal officials have been investigating 122 bomb threats called into nearly 100 JCC schools, child care and other similar facilities in three dozen states. Two law enforcement officials told ABC News that Thompson is not believed to be the main suspect behind the scores of recent bomb threats.
The arrest comes as the FBI was growing increasingly worried about such incidents. Agents feared the volume could be lulling people and lead people to start ignoring the threats and stop evacuating facilities.
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The NYPD also was worried that evacuations were creating large groups outside that could become targets for shooting or ramming.
"The defendant caused havoc, expending hundreds of hours of police and law enforcement resources to respond and investigate these threats. We will continue to pursue those who peddle fear, making false claims about serious crimes," said New York City Police Commissioner James O'Neill. "I'm grateful for the collaboration between the NYPD detectives, FBI agents, and prosecutors whose cross-country investigation led to this morning's arrest."
The Associated Press contributed to this report.