The authorities will now go for DNA testing of the couple to determine if they are her parents.
In-charge district collector Ruchika Chauhan said that Geeta used sign language to convey that it was not her family.
She said, "Geeta conveyed that she worshipped Hindu deities- Lord Shankar and Hanuman- and does not belong to a Muslim family."
The family is from Mirajpur village in Bihar's Saran district and had claimed that Geeta is their long-lost daughter Rubeida who went missing when she went out to watch a marriage procession.
Chauhan, however, said that DNA samples of Mohammad Isa and his wife Julekha Khatoon have been collected for verification.
The family members, meanwhile, have not lost hope with Mohammad Isa's son Himtaj telling reporters that Geeta failed to recognize his father possibly because she had stayed away from the family for a long time.
"There are many temples along with a mosque around our house and Hindus and Muslims celebrate each other's festivals together. We visit Hindu families during the festival of Chhath," he said.
"There may be the memories of worshipping deities in Hindu temples in her subconscious mind," Himtaj added.
"We hope that the DNA examination will clear the situation," Himtaj said.
District collector Chauhan informed that the DNA verification process would be the same even if Geeta recognises anyone as her parent.
Earlier Geeta had met a family from Sokha Kishku village of Jamtara district of Jharkhand but she did not recognise them either, said Chauhan.
The DNA samples of the couple have also been sent for verification, she added.
Geeta was found by Pakistan Rangers on the Samjhauta Express at the Lahore railway station when she was around seven years old. Karachi-based Edhi Foundation looked after her while she was in Pakistan.
After returning to India in October 2015, Geeta has been living at an institution for hearing impaired children run by an NGO here.
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