n the jittery days following September 11, FBI Director Robert Mueller was receiving threat briefings from both the FBI and the CIA. Mueller asked to have the two threat lists combined, but CIA bureaucrats resisted–until he went over their heads with a phone call to CIA Director George Tenet.

After the catastrophic terrorist attacks, government agencies banded together to fight al Qaeda. The results were swift–a global roundup of some suspected al Qaeda operatives. Still, it's been a struggle at times to get the FBI and CIA to overcome their history and divergent cultures. Complicating matters: A congressional inquiry into possible intelligence failures preceding 9/11 was turning up evidence that the two agencies had failed to adequately share information. The revelations triggered a round of public sniping.

But this pales in comparison with the days of FBI Director J. Edgar Hoover, who barred contacts with the CIA. "There was a time when the CIA and FBI worked at cross-purposes," says a senior intelligence official. Progress was nearly derailed in 1994, when the FBI unmasked CIA officer Aldrich Ames as a Soviet spy.

Since then, cooperation–which has always been better in the field than in Washington–has improved. CIA and FBI officials do regular duty at each other's agencies. Congress loosened several laws on the kind of information the FBI could share with the CIA. Still, the gumshoes and spooks are finding that their two missions continue to clash. "You have a law enforcement culture, which guards information for prosecution, and an intelligence one, which is based on disseminating information," says former CIA deputy director for operations Jack Devine.

Today, both agencies are under the gun, especially with scrutiny from Congress. Mueller has embarked on a massive reorganization, making the prevention of terrorism the FBI's top priority. Tenet, aware that some in Congress want his scalp, has ordered the CIA to beef up its pool of linguists and to ease rules on the recruitment of foreign agents with sordid pasts.

Part of the problem was structural. The 9/11 attacks have helped break down the clear lines that gave the FBI domestic responsibility while the CIA operated abroad. "There has to be a seamless process of sharing information," says Oliver "Buck" Revell, a former FBI deputy director.

One important step: When senior CIA officials meet daily at 5 p.m. to review the latest steps in the war on terrorism, the FBI is now at the table, too.