The federal jury on Tuesday convicted underboss Joseph "Moussie" Massimino and two others of racketeering, and convicted a mob associate of two loansharking counts.
But the jury acquitted or deadlocked on most counts against the seven defendants.
Defense lawyers see the verdict as a slam of the government's 13-year investigation into illegal gambling, video poker machines and loansharking in South Philadelphia.
The jury heard one defendant say on a secret FBI recording, "It's a broke, broke mob."
Lead defense lawyer Edwin Jacobs Jr. calls the prosecution "an enormous waste" of taxpayer money.
Federal prosecutors call the case important and say they will consider retrying the unresolved counts.
The jury had been deliberating for 21 days, but a newly constituted panel had been at work only for 12 days.
The jury suffered several setbacks. Two jurors had been replaced since deliberations began Jan. 8, forcing the group to start anew each time.
And a foreman stepped down, an apparent sign the deliberations were taking a toll on him.
The Ligambi trial started in October.
Federal authorities believe Ligambi, 73, has quietly controlled the mob in Philadelphia and southern New Jersey for more than a decade, since flamboyant young boss Joey Merlino went to prison in 1999. Merlino was paroled last year and has settled in South Florida. His father died in prison in October, and his mother has occasionally attended the Ligambi trial.
Given the violent history of La Cosa Nostra, the jury has been seated anonymously and is brought to court each day from a remote location. Defense lawyers, though, frequently note that there have been no mob killings or shootings in Philadelphia in the past decade. One dubbed the latest attempt to thwart organized crime in the city "Mob Lite."