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(CNN) —  

When Aaron Fraser began excavating behind his childhood home in Jacksonville, Florida, as part of a renovation in 2014, he made a gruesome discovery: human remains.

They were the skull and bones of his mother, Bonnie Haim, who had gone missing in January 1993 and whose body had not been found.

Prosecutors say that discovery led officials to arrest her then-husband, Michael Haim, and charge him with second-degree murder.

“The truth was always out there, buried in their backyard,” Assistant State Attorney Alan Mizrahi said in opening statements in the murder trial on Tuesday.

Michael and Bonnie Haim had been having marital problems, and he has long been a prime suspect in the case, his defense attorney Janis Warren said in her opening remarks.

But he has maintained his innocence since her disappearance. In an interview with CNN affiliate WJXT shortly after Bonnie Haim disappeared in 1993, Michael Haim said she left their home on the night of January 6 after a relationship issue.

“Basically she just wasn’t happy and she wanted to leave, and I couldn’t stop her from leaving,” he told WJXT.

Michael Haim is accused of killing his wife, Bonnie Haim, in 1993.
Michael Haim is accused of killing his wife, Bonnie Haim, in 1993.
PHOTO: WJXT

Warren said prosecutors did not have enough evidence to prove his guilt beyond a reasonable doubt.

“We agree she’s dead. We agree that’s her body in the backyard. But they have to prove to you that he did it,” she said. “When you listen to the evidence, ladies and gentlemen, and when you’re finished, you’re gonna see the lack of evidence in this case far outweighs any evidence they brought you.”

The childhood memories of Fraser, who was 3 when his mother disappeared, are expected to be a major part of the case against Michael Haim, CNN affiliate WJXT reported.

After his mother disappeared, he told a child welfare worker at the time, “Daddy hurt Mommy,” WJXT reported.

“Aaron also stated that ‘Daddy shot Mommy’ and ‘My daddy could not wake her up,’” a 2015 arrest affidavit said, according to WJXT.

Opening statements in the trial

Bonnie Haim’s remains were found under a shower pallet in the home’s backyard, Mizrahi said. A .22-caliber shell was also found near the body, he said, and Michael Haim owned a .22-caliber rifle.

Although a medical examiner could not affirmatively determine how she was killed, Mizrahi argued that Michael Haim shot her and then buried her there in 1993.

“The defendant’s actions before the killing and after the killing demonstrate his depraved indifference to Bonnie Haim’s life,” he said.

Investigators had searched the property several times in the years after her disappearance, but did not find her remains until Fraser’s discovery two decades later.

“That was the piece of the puzzle that we really felt we were missing,” Jacksonville Sheriff’s Office Director Mike Bruno told WJXT in 2015. “There are so many unsolved or cold cases that are in this same situation of we just need that one clue, that one tip, that one piece. Here, we were able to get it, and to start that piece of closure.”

Warren, Haim’s attorney, said on Tuesday that prosecutors would not be able to prove that he killed her and placed her body there on the night she disappeared.

“The only thing that’s important is: Can they prove he killed her? And can they prove he put the body in the yard? There’s no evidence of either one of those,” she added.