Kirsten Hatfield, 8, disappeared from her home in Midwest City one night in May 1997.
Police said the second-grader's bedroom window was cracked and her underwear was found in the backyard, according to CNN affiliate KOKH.
The child has never been found, Midwest City Police Chief Brandon Clabes said Tuesday at a news conference.
A former neighbor of the girl, 56-year-old Anthony Joseph Palma, was arrested Monday and charged with kidnapping and first-degree murder. Authorities filed the murder charge because they believe Kirsten is dead, Clabes said.
Authorities were led to Palma after a new investigator assigned to the case last June realized the FBI or the Oklahoma State Bureau of Investigation had never tested some of the evidence, Clabes said.
Using DNA technology that is more advanced than it was in 1997, lab technicians discovered blood from the window sill and the girl's underwear came from an unknown male, he said. Investigators ran that DNA through a national database and didn't find a match.
Authorities then tracked down about 10 men who'd previously been questioned and asked for DNA samples, Clabes said.
One of them was Palma, who lived just two doors down from the Hatfield house and had been interviewed twice in 1997, Clabes said.
Palma told investigators he was in bed the night Kirsten disappeared but awoke about 2 a.m. because a dog was barking, KOKH reported.
He said he wasn't involved and allowed police to take a new DNA sample with a cheek swab, KOKH said.
His sample matched the DNA on the underwear and the window sill, the chief said.
Palma lived alone in 1997, the chief said, but married in 1999 and still lives in the same house with his wife and children. He'd been working as a groundskeeper.
The Hatfield family moved away from their home in Midwest City.
Chris Hazen, who married Kirsten Hatfield's mother, Shannon, two years after the disappearance, spoke to the media Tuesday and thanked police for not giving up.
"This has been a terrible nightmare to my wife since it happened," he said.