The matter came to light this evening after bodies of both the boy and the girl were fished out by the police.
The name of boy is given as Nikhil Ratnapal Meshram (18) and that of the girl as Tabbu Shahnaj Pyaru Sheikh (15), both residents of Ambedkar ward in Desaiganj.
Both the boy and the girl were missing from their houses for the last two to three days, after which the girl's mother lodged a complaint yesterday at the Desaiganj police station, the police said.
When relatives began searching for the girl, they found bodies of Tabbu and Nikhil floating in a well near the Mata ward of Desaiganj. The matter was immediately reported to the police, who rushed to the spot and fished out their bodies from the well.
The bodies were found with the hands of the boy and the girl tied to each other with a scarf (duppata) of the girl, eye-witnesses said.
The Desaiganj Police registered a case of accidental death and are investigating the matter further.