A 46-year-old man was indicted yesterday for killing the mother of his son, more than two decades after the 21-year-old woman was murdered, Bronx prosecutors said.

Jonathan Jolivert, 46, was charged with second-degree murder for the death of 21-year-old Michelle Page Gilliam.

Jolivert, who's DNA matched that found under Gilliam's fingernails, pleaded not guilty during his arraignment in Bronx Supreme Court Tuesday. An attorney for Jolivert did not immediately return a request for comment.

On March 24, 1993, Jolivert allegedly stopped by Gilliam's apartment near Morris Avenue and East 168th Street to drop off child support money, prosecutors said. Their son, who was 14 months old at the time, was not home.

The Manhattan Community College business student was found strangled with a scarf, with a kitchen knife still protruding from her throat.

Gilliam's mother, who lived there with her, found her daughter naked on the floor when she returned home, prosecutors said.

The NYPD's cold case Squad took over the cases and detectives arrested Jolivert at a drug treatment facility in Carmel, New York, on Feb. 13.

His next court appearance is scheduled for June 11.