The then-unidentified girl's body was found in a ditch along the A10 freeway close to the city of Blois in central France in August 1987.
The girl, whose mutilated body had marks of long-term abuse, was known in France as the "little martyr of the A10." Her photo was circulated to authorities in 30 countries around the world.
Blois prosecutor Frederic Chevallier said that a breakthrough has been possible in the case that baffled authorities for years "because of the evolution of science and DNA."
The parents, who are both in their 60s, were identified and tracked by chance through their son's DNA, which was tested in an unrelated 2016 case and matched him as the dead girl's brother, Chevallier said.
The parents were arrested by French authorities on Tuesday.
"Inass Touloub has at last a name," Chevallier said.
The girl was born in July 1983 in Casablanca, Morocco, and was the third of seven children, Chevallier said.
The father said he was "relieved" that he had been arrested that "he was scared of his wife and lived under her domination," Chevallier said.
The mother gave an erratic account to authorities, claiming at one point that the girl was still alive, Chevallier added.
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