JACKSON (AP) — Two 3-year-old girls disappeared from their homes in the early 1990s and were later found sexually assaulted and murdered. The brutal slayings were separated by 18 months, but the crimes are linked by striking similarities.

Both attacks happened in Noxubee County, a rural and economically strapped farming community, in eastern Mississippi. In each case, the boyfriends of the children’s mothers were convicted of the crimes. One was sentenced to death and the other to life imprisonment.

Now a one-time suspect who was never charged with the crimes has confessed to murdering both girls, according to the Innocence Project, a nonprofit group of attorneys that tries to help inmates who are thought to have been wrongfully convicted.

Justin Albert Johnson was charged Monday with capital murder in the 1992 rape and strangulation of 3-year-old Christine Jackson.

Johnson was linked to Christine’s murder in 2001 when the Innocence Project sent a blood sample — taken soon after the 1992 killing — for DNA testing, said Innocence Project attorney Vanesa Potkin. His DNA allegedly matched semen found on Christine’s body.

The blood sample used in the test had been preserved at the Mississippi State Crime Laboratory for years.

Another dramatic revelation was made Friday when the New York-based Innocence Project said that Johnson allegedly confessed to authorities not only to killing Christine, but also to the 1990 sexual assault and murder of 3-year-old Courtney Smith.

‘‘He confessed to both murders, both abductions, both sexual assaults and he also informed investigators with the attorney general’s office that he acted alone in both cases,’’ Peter Neufeld, co-director of the Innocence Project, told The Associated Press on Friday.

Johnson, a 51-year-old Brooksville resident, was arraigned Tuesday, pleaded not guilty and was being held without bond, said Attorney General Jim Hood. It was not clear if Johnson had hired a lawyer. Neufeld said Johnson talked to authorities about both killings on Tuesday.

Ben Creekmore, a district attorney now involved in one of the cases, declined to ‘‘characterize it as a confession for legal reasons.’’

‘‘He gave a statement with respect to the facts,’’ Creekmore told The AP.

Creekmore said his office is ‘‘preparing a motion to dismiss and discharge’’ murder charges against Kennedy Brewer. The motion will be presented to a judge in a hearing tentatively scheduled for late next week.

Brewer was convicted of killing Christine and was sentenced to death in 1995. But in 2001, the DNA tests from the original blood samples linked Johnson — not Brewer — to the slaying and Brewer was released on bond last August pending a new trial, Potkin said.

Levon Brooks, now 48, was convicted in Courtney’s death in 1992 and was sentenced to life.

District Attorney Forrest Allgood prosecuted both men. However, he has since recused himself from handling Brewer’s case because one of Brewer’s former lawyers now works for him, Hood said.

Allgood did not immediately respond to a message Friday seeking comment on how the alleged confession would affect Brooks’ case.

Both children were taken from their homes in the middle of the night. The body of one child was found in a pond, the other in a creek. The same dentist — Dr. Michael West — testified in both cases that he linked the suspects to the murders through bite marks found on the bodies.

The marks were caused by decomposition, the bodies being in water and animals — not human teeth, the Innocence Project and lawyers for the men claim.

‘‘My position is that Dr. West has been thoroughly discredited through this process,’’ said Brewer’s attorney, Carrie Jourdan.

West did not respond to a message left Friday at his office.

Neufeld was also critical of West and State pathologist Dr. Stephen Hayne, accusing both doctors of misconduct in the Brewer and Brooks cases.

Hayne said he did not know why he’s ‘‘being attacked because I didn’t link anybody to this.’’

‘‘All I did was present the facts that I saw,’’ Hayne said. ‘‘I did the post-mortem examinations. I didn’t link them or exclude them.’’