The ex-boyfriend of Megan McDonald — the 20-year-old daughter of an NYPD detective found bludgeoned to death upstate two decades ago — has been arrested and charged with her murder, state police announced Thursday.

Edward Holley, 42, of Orange County, is accused of slaying his estranged girlfriend on March 14, 2003, shortly after the SUNY college student sought to buy marijuana from him, state troopers said.

McDonald — the daughter of former detective Dennis McDonald, who died a year before his daughter was killed — was last seen pulling into an upstate apartment complex.

Her remains were later found in a field off Browser Road.

In a statement Thursday, the NYPD’s Detectives Endowment Association praised state troopers for solving the 20-year-old death of the daughter of one of their own.

“The Detectives’ Endowment Association is grateful to our NYS Police partners for their unrelenting commitment to justice for Megan McDonald, daughter of a retired Detective,” the union said on Twitter.

“The union was at their side throughout the investigation — and standing shoulder-to-shoulder with Megan’s family.”

Police said Holley and a second unidentified suspect who died in 2010, killed McDonald days after she attempted to end a relationship with Holley, according to a criminal complaint.

“The victim and Edward Holley were involved in a romantic relationship, and she attempted to end their relationship several days before the murder,” state police Investigator Michael Corletta wrote in the complaint filed Wednesday.

Police said Holley later admitted the two had argued.

“Although the reasoning for this argument changes in all his state police interviews, Holley consistently advised that he and the victim were involved in an altercation several days prior to the homicide which Holley claimed was the last time that he saw the victim,” Corletta said.

But cops said McDonald reached out to Holley the day before her murder.

“The victim was looking to acquire marijuana just prior to her murder and Edward Holley was the victim’s main marijuana supplier,” the complaint said.

Interviews conducted by state police investigators “lead to the inference that as a last resort the victim acquired or intended to acquire marijuana from Holley shorter after her last outgoing call at 12:20 a.m.” on March 13, 2003, according to the complaint.

McDonald had just left a friend’s party to meet up with Holley, the complaint said. Then, she disappeared.

Investigators determined that McDonald was killed while sitting in the driver’s seat of her 1991 Mercury Sable, with her body dumped along a dirt path on Bowser Road in Wallkill, police said.

Holley lived just 500 feet from where McDonald’s car was later found.

“Based on my review of the records associated with this case, numerous interviews and my experience as a law enforcement professional, there is probable cause that on March 14, 2003, Edward V. Holley did intend to cause the death of another person, Megan McDonald, and he did in face case the death of such a person,” Corletta wrote in the complaint.

McDonald worked at a cafe at the Galleria Mall while attending classes at SUNY.