Rasul Magomedov recognized his missing daughter Maryam after being shown photos of the remains of the unidentified suicide bomber, the website said.
More than 50 people have been killed in suicide attacks in Russia over the past week, both in the Moscow metro by bombers Russian media have dubbed 'black widows', and in a town in the turbulent North Caucasus region of Dagestan.
Fears of a new bombing campaign against the Russian heartland increased after a double bomb attack on a railway line on Sunday which security forces said was linked to the earlier attacks.
"My wife and I immediately recognized our daughter Maryam. When my wife last saw our daughter she was wearing the same red scarf we saw in the pictures," Magomedov, a teacher from the village of Balakhany in Dagestan told Novaya Gazeta.
Magomedov said his daughter graduated with a degree in mathematics and psychology from the Dagestan Pedagogical University in 2005. She returned to her village, lived at home and taught computer science at a local school.
"I would really like the investigation to uncover the true picture of what happened. We cannot even suggest how Maryam could get to Moscow. Yes, she was religious. But she never expressed any radical beliefs," he said.
Magomedov said his daughter had denied to him local security force allegations that she had links to insurgents in the region or had married a local separatist leader.
The family came under the scrutiny of the security forces two years ago, when a brother of Maryam was charged with belonging to an armed group and allegedly tortured in custody before most charges were dropped.
The first bomb, which Magomedov believes was carried by his daughter, tore through a packed Moscow metro train just before 8 a.m. on Monday as it stood at the Lubyanka station, close to the headquarters of the FSB. It killed at least 23 people.
A second bomb was detonated less than 40 minutes later in a train waiting at the Park Kultury metro station, killing at least 12 people. More than 70 people were taken to hospital after the two attacks.
"Maryam was a calm and self-confident person who always loved to learn. She co-authored three scientific works. No one ever noticed any extremist expression or inappropriate conduct by her," a person close to her family was quoted by the newspaper as saying.
Photographs of a second young woman, obtained by Reuters from a law-enforcement official in Dagestan, showed her dressed in a black hijab and holding a grenade. Another photograph showed this other woman holding a pistol.
She was named on Friday as Dagestani-born Dzhennet Abdurakhmanova, the widow of 30-year-old Umalat Magomedov, a prominent insurgent killed by Russian forces on December 31, according to sources who did not want to be identified.
Russia's FSB security chief Alexander Bortnikov has blamed militant groups linked to the North Caucasus for the attacks but given no further details on the investigation.
Islamist Chechen rebels claimed responsibility on Wednesday for the Moscow metro bombings and threatened further attacks against Russian cities.
