Genetic profiles of Sasha Ruseva and her husband Atanas matched that of the girl, said Svetlozar Lazarov, a Bulgarian interior ministry official.
Ruseva, 35, has said she gave birth to a baby girl four years ago in Greece while working as an olive picker, but gave the child away because she was too poor to care for her.
Maria has been in temporary care since last week after authorities raided a Roma settlement in central Greece and later discovered that girl was not the child of a Greek Roma couple she was living with.
The Greek couple, Christos Salis, 39, and Eleftheria Dimopoulou, 40, have been arrested and charged for allegedly abducting Maria, as well as document fraud.
A lawyer said they plan to seek legal custody of the fair-haired girl. The couple have told authorities they received Maria after an informal adoption.
Under Greek law, child abduction charges can include cases where a minor is voluntarily given away by its parents outside the legal adoption process.
"Now that they're in prison there's not much they can do," their lawyer, Costas Katsavos, said.
"But provided what we said is borne out, that it was not an abduction, then logically they will be released from prison and they will be able to enter a proper (adoption) process."
Costas Yannopoulos, director of the Greek children's charity Smile of the Child, which has been looking after the girl, had no comment on her fate, saying only: "We are dealing with the humanitarian side of this issue, looking after a young girl."