The FBI is investigating failed bank IndyMac (IMB) for possible mortgage lending fraud.

It’s not clear when the investigation began. On Wednesday, the FBI said it had added 2 companies to those already under investigation, bringing the total number to 21.

Bank regulators seized the Pasadena-based bank on July 11 after panicked depositors sought to withdraw their money. It was the third largest banking failure in U.S. history. The bank now operates under the name IndyMac Federal Bank, FSB.

Overall, the banking system appears to be in less danger now than it was in the late 1980s and early 1990s when about 1,000 federally insured institutions failed in the savings-and-loan debacle.

“We receive information from a variety of sources on a daily basis, and we have an obligation to review each allegation on its merits,” says Jason Pack, a spokesman for the FBI.

The FBI’s investigation of IndyMac is believed to focus on accounting fraud.

Few targets of the nationwide investigation have been identified, but one of them is Countrywide Financial, recently acquired by Bank of America (BAC).

After the FBI announced its probe, Goldman Sachs (GS), Morgan Stanley (MS) and Bear Stearns, since acquired by JPMorgan Chase (JPM), said they’d been asked to provide information. But the FBI declined to comment on any possible role played by the investment banks. Last year, Beazer Homes (BZH) said it had received a federal grand jury subpoena seeking information about its mortgage business.

David Barr, a spokesman for the Federal Deposit Insurance Corporation, declined to comment.

The FDIC insures depositors up to $100,000 per bank. The limit was last increased in 1980 and will be raised in 2010 with the new limit pegged to inflation. Some retirement accounts are insured up to $250,000.

Shortly after the FDIC took over IndyMac, most depositors received immediate access up to $100,000 in their account and 50% of any money in excess of that amount. Depositors received certificates for any money they couldn’t immediately withdraw and may be able to receive some of that money when the bank’s assets are sold.

Many big savers rushed to withdraw money in excess of the $100,000 limit from Indymac, but that’s not necessary with a CDARS account.