The investigation into the 1993 slaying of South Boston nightclub owner Steven DiSarro ramped up Friday as a second man was charged with the murder, along with former New England Mafia Boss Francis “Cadillac Frank’’ Salemme.

A federal indictment unsealed Friday charges Paul Weadick, a 61-year-old plumber from Burlington, and 83-year-old Salemme with killing DiSarro, who was described as a witness in a federal investigation that was targeting the mobster and his son.

The indictment says that Salemme and his late son had a hidden interest in The Channel, a now-defunct nightclub acquired by DiSarro in the early 1990s.

DiSarro “had knowledge of various criminal activities in which the Salemmes were involved’’ and was killed to prevent him from providing information to law enforcement officials, according to the indictment.

Salemme, who had been quietly living as Richard Parker in Atlanta after being relocated there through the federal witness protection program, was arrested several weeks ago on a complaint charging him with the decades-old slaying. He remains jailed without bail and is slated to be arraigned Thursday on the new indictment.

Weadick was arrested Friday morning and appeared briefly in US District Court in Boston, where he pleaded not guilty to the one-count indictment charging him with murdering a witness.

“My client has absolutely nothing to do with the murder of Mr. DiSarro,’’ Weadick’s attorney, Carmine Lepore, told reporters after the hearing. He described Weadick as “an innocent man’’ and said he has been charged based on lies told by notorious gangster Stephen “The Rifleman’’ Flemmi.

US Magistrate Judge Donald L. Cabell ordered Weadick held without bail pending a hearing Thursday on whether he should remain jailed until the case is resolved.

Salemme and Weadick are the first to be charged with the murder of Di­Sarro, a former Westwood resident and father of five who was 43 when he vanished on May 10, 1993, and was presumed murdered. Investigators, acting on a tip, discovered DiSarro’s remains in March, buried in a Providence lot owned by a man facing federal drug charges.

A third man, Rhode Island mobster Robert “Bobby’’ DeLuca, was indicted in June on charges of obstruction of justice and making false statements for allegedly denying any knowledge about DiSarro’s disappearance. That indictment alleges that DeLuca helped dispose of DiSarro’s body.

Flemmi, who is serving a life sentence in prison for 10 murders and was a longtime associate of Salemme and James “Whitey’’ Bulger, told authorities in 2003 that he walked in on DiSarro’s murder at the Sharon home of Salemme’s estranged wife, according to a US Drug Enforcement Administration report filed in federal court.

Flemmi said Salemme’s son, Frank, was standing behind DiSarro with his arms around his throat, choking him as he lifted him off the floor.

Flemmi also observed Weadick “grab DiSarro’s legs and hold them off the ground’’ so he couldn’t support himself as he was strangled, according to the DEA report.

The elder Salemme and his brother, John, watched DiSarro being killed, according to Flemmi.

Flemmi said he fled because he didn’t want to be involved in a Mafia-related murder, then Francis Salemme Sr. later told him that DiSarro’s body was buried at a Rhode Island construction site.

According to Flemmi, Weadick was a close friend of the Salemmes and was also involved in the construction and management of The Channel. Salemme’s son, Frank, died in 1995 of lymphoma.

By the time Flemmi offered his account of the slaying, the elder Salemme had already been placed in the federal witness protection program for cooperating with the prosecution of Bulger and his corrupt FBI handler, John. J. Connolly Jr.

Salemme was kicked out of the program in 2004 when he was indicted for lying and obstruction of justice for previously denying any knowledge about DiSarro’s slaying. He pleaded guilty and was allowed back into the program in 2009 after serving a five-year sentence.

After Salemme’s arrest last month, his lawyer said Salemme denies he killed DiSarro and “is ready to fight this case tooth and nail.’’

John R. Ellement of the Globe Staff contributed to this report. Shelley Murphy can be reached at shmurphy@globe.com. Follow her on Twitter @shelleymurph.