Republican attitudes toward the law enforcement agency have grown more negative over the past year.
Trump has said the FBI disliked Comey, but the emails suggest otherwise.
The letter, 11 days before the election, has been widely cited as one of the potential reasons Clinton ultimately lost to Trump.
McCabe's departure comes as Trump and Republicans step up attacks on the top law enforcement agency.
In a heated phone call, Trump reportedly lashed out at the wife of Andrew McCabe, who stepped down as FBI deputy director Monday.
Bowdich was associate deputy director under Comey and was involved in the response to the San Bernardino shooting.
Trump and his allies had scrutinized McCabe for campaign contributions his wife once received.
Former FBI Director James Comey, whose controversial decisions—from the Clinton letter to the Trump memos—have been excoriated by both Democrats and Republicans, will begin teaching a college ethics course in the fall.
President questioned top FBI lawman on how he voted, raising concerns amongst former officials.
Robert Mueller reportedly wants to know more about Comey's Trump memos.
The Department of Justice said on Friday that President Donald Trump did not invite his maligned attorney general to a legislative discussion group at Camp David this weekend.
A former U.S. attorney now says the attorney general "must go" if a new report saying he tried to undermine the Trump-Russia investigation is true.
Republicans called for Sessions to step down this week; other critics say his position in the Department of Justice "isn't tenable."
Tweets threatening political rivals, North Korea, Pakistan and others pose a threat to America, say experts.
Public figures including John Brennan and Joe Scarborough have said they donated.
The president has called out James Comey and Andrew McCabe.
The FBI had previously confirmed the existence of the drafted statement.
The former attorney general and former president met in Phoenix while the FBI was investigating Hillary Clinton's use of a personal email server.
Wray appeared before the House Judiciary Committee after Trump said the reputation of the bureau was "in tatters."
Representative Matt Gaetz and others are calling for answers about Comey's handling of the Clinton emails probe.