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 The Cape Girardeau County prosecutor's office issued a one-paragraph statement saying police had found the body on Wednesday.
"It has been confirmed that the body is that of Jacque Sue Waller," the statement read. It didn't say where or how the body was found. A woman answering phones at the prosecutor's office said no further comment would be made, citing an ongoing investigation.
Waller and her estranged husband, Clay Waller, had nearly finalized a divorce when she disappeared on June 1, 2011. He was charged last year with first-degree murder and faces trial in September.
Jacque Waller's sister, Cheryl Brenneke, has custody of their 7-year-old triplets.
In a statement on their Facebook page Waller's family confirmed "with a heavy heart" that Jacque Waller's remains were found. The statement said funeral arrangements have not been made.
"We thank everyone of you who has supported us and assisted us in this terrible nightmare," the statement read.
Messages seeking comment from a spokeswoman for Waller's family were not returned, but Brenneke told the Southeast Missourian newspaper that she was in shock.
"You anticipate how you're going to feel for two years," Brenneke said. "You just can't prepare yourself, really. You just can't."
Authorities said the couple had been living apart for about three months -- she was living in Ste. Genevieve County, he was living in Jackson. They met with an attorney about divorce proceedings on June 1, 2011. Police said they argued then about financial problems.
By that evening, Jacque Waller's relatives were becoming worried because they had not heard from her. Her father, Stan Rawson, has said his daughter had previously confided to Brenneke that Clay Waller had threatened her.
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 Jacque Waller's Honda Pilot was found along Interstate 55 a day after she disappeared. Several searches since then have turned up sporadic leads, including the discovery of her purse near where the car was found.
The FBI said last year that Clay Waller suggested to his father that he had broken Jacque Waller's neck and buried her in a hole that he had dug in advance. But Clay Waller has not made any confession to police, and his father died before he could testify.
At a preliminary hearing in July on the murder charges against Clay Waller, then-prosecutor Morley Swingle outlined a case built largely around circumstantial evidence: potential motives of both jealousy and greed; blood splatter found at Clay Waller's house; apparent efforts to hide a blood-stained carpet in a crawl space; and Waller's history of anger and resentment toward his wife.
During the hearing, Edwin Rhodes, an acquaintance of Clay Waller, recalled that about two months before Jacque Waller's disappearance, Clay Waller told him, "I ought to just kill her."
Clay Waller pleaded guilty in late 2011 to threatening Brenneke over the Internet. He is serving a five-year federal term.
[Associated
Press; By JIM SALTER]
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