For the third time in less than a year, the Justice Department has busted out the Civil War-era False Claims Act to sue a major bank for fraud in connection with the mortgage crisis. This time, there’s a whistleblower involved that stands to take home a big share of the government’s recovery.

Citigroup agreed on Wednesday to pay $158.3 million to resolve allegations first raised last year in a sealed lawsuit brought by whistleblower Sherry Hunt, an employee of CitiMortgage Inc. in Missouri. The settlement, announced by the Manhattan U.S. Attorney’s Office, came a week after Bank of America agreed to pay $1 billion to resolve False Claims Act mortgage fraud claims brought by federal prosecutors in Brooklyn. The Justice Department is continuing to press claims similar to those in the BofA case, meanwhile, in a False Claims Act suit that Manhattan prosecutors filed in May against Deutsche Bank AG.

Wednesday’s settlement resolves claims that Citi falsely certified to the U.S. Department of Housing and Urban Development that shoddy loans qualified for mortgage insurance. “Lenders with authority to directly endorse FHA-insured mortgages must be serious about applying our underwriting guidelines and implement a quality control program that ensures compliance,” HUD General Counsel Helen Kanovsky said in a statement on the Citi settlement. “This is a federal program and lenders who violate these requirements face potential False Claims Act liability.”

The settlement signals prosecutors’ continued use of the False Claims Act to hold banks accountable for the failures of the mortgage boom. And its the first of the cases based directly on whistleblower claims under the law’s qui tam provisions. According to the complaint, Hunt is still employed at Citi and was a quality control manager focusing on FHA loans. (A Citi spokesperson declined to comment on Hunt’s current employment status.)

For their efforts, Hunt and her lawyers are in line to receive a big chunk of Wednesday’s settlement. According to court records, the government has agreed to pay nearly $31.7 million, or 20 percent, of the settlement to Hunt. Her lawyer, Finley Gibbs of Rotts & Gibbs, did not respond to a request for comment.

Manhattan federal district court judge Laura Taylor Swain sealed Hunt’s complaint in August, a month after the Justice Department subpoenaed Citigroup. The new complaint that the Justice Department unveiled Wednesday is filled with internal Citi e-mails that prosecutors cite to claim that business production units at the bank applied “brute force” to pressure quality control managers to downgrade findings of mortgage fraud. Of the 30,000 loans comprising $4.8 billion in obligations that Citi asked the FHA to insure since 2004, 30 percent have defaulted, the complaint asserts.

Brad Karp of Paul, Weiss, Rifkind, Wharton & Garrison, who represented Citi alongside partners Theodore Wells Jr. and Joyce Huang, was unavailable for comment. Citi spokesman Mark Rodgers said in a statement that the bank takes its “quality assurance processes seriously” and has “pro-actively undertaken process improvements to ensure that they are as robust as possible.”

Both Citigroup and the Justice Department characterized the settlement as part of the larger $25 billion national mortgage accord reached last week with five banks, the Justice Department and state attorneys general. Citi separately pledged $2.2 billion as part of the foreclosure settlement.