Juan Thompson, 31, was taken into custody on Friday morning in St. Louis and was expected to make an initial court appearance there later in the day.
It was not immediately clear whether investigators believe Thompson is responsible for all of the more than 100 threats that have been made by phone to Jewish community centers in dozens of states since January.
The Anti-Defamation League (ADL) tweeted the news Friday, saying, " FBI, NYPD, and NYS police told us arrest made in bomb threats against ADL; several other Jewish institutions. Thx 2 them!More info as get it."
The ADL itself was the target of a hoax bomb threat last week.
In a criminal complaint filed in federal court in Manhattan, authorities accused Thompson of making at least eight threats, mostly by email.
Prosecutors said Thompson made the threats in an effort to harass a former girlfriend by telling the Jewish groups she was the person behind the alleged bombs.
After the woman broke up with him in July 2016, Thompson began a sustained harassment campaign in retaliation, authorities said.
A day after the relationship ended, Thompson sent an email purporting to be from a producer at a national news organization to her boss at a social service company in New York, according to the complaint. The email claimed she had been pulled over for drunk driving and sued for spreading a sexually transmitted disease.
In the following weeks, the woman received messages from a purported relative of Thompson, falsely claiming Thompson was on his deathbed after a shooting.
Thompson later threatened to publicize nude photos of her and told her employer she had threatened his life, prosecutors said. He also sent a message to a national children's welfare organization, claiming she admitted watching child pornography.
In late January, Thompson began emailing bomb threats to Jewish groups using his own name and claiming she had hacked his account. He also sent threats pretending to be her, according to the complaint.
On Feb. 24, he posted on Twitter, "Know any good lawyers? Need to stop this nasty/racist #whitegirl I dated who sent a bomb threat in my name."
Prosecutors said part of his motive was to portray his ex-girlfriend as an anti-Semite. He sent one email calling for a "Jewish Newtown," referring to the 2012 school massacre in Connecticut.
It was unclear whether he shared those sentiments, and his recent Twitter posts did not appear to include any explicit anti-Semitic thoughts.
Jewish community centers and schools in the United States have received five waves of hoax bomb threats this year, stoking fears of a resurgence in anti-Semitism.
US President Donald Trump, Israeli officials and Jewish groups have all condemned the surge in intimidation as well as cases of vandalism targeting Jewish cemeteries.
Police said last weekend that about 100 headstones were toppled at a Jewish cemetery in Philadelphia, about a week after a Jewish cemetery in St. Louis was vandalized.
Some Jewish groups see the vandalism and threats as a sign that anti-Semitic groups have been emboldened by Trump's election. His campaign last year drew the support of white supremacists and other right-wing groups, despite Trump's disavowals of them.