There were conflicting reports about Mayes' fate since he was found after suffering an apparently self-inflicted gunshot wound Thursday night in Union County, Mississippi, CNN reported.
Daniel McMullen, FBI special agent in charge in Jackson, told reporters around 10 p.m. that Mayes was pronounced dead.
The two surviving sisters are suffering from the experience of being out in the woods and from being kidnapped. They are suffering from dehydration and exhaustion, but appear OK, a federal law enforcement source on the scene told CNN.
Mayes, 35, was on America's Most Wanted Fugitive List.
Guntown Police Chief Michael Hall said a SWAT team found Mayes and when they moved in, he shot himself.
Police say the two daughters that Mayes allegedly abducted, Alexandria Bain, 12, and Kyliyah Bain, 8, were found alive and safe. Both girls were being taken to a hospital for observation.
Authorities responded to the area after someone called to report what they suspected was Mayes' vehicle, a law enforcement source close to the investigation said Thursday night.
A task force was nearby and as they approached, Mayes stood up and shot himself in the head, the source said. The two girls were not near him at the time.
When they found Mayes he was still alive, but he later succumbed to his wounds.
Mayes and his wife, Teresa, were charged with first-degree murder in the deaths of Jo Ann Bain, 31, and her daughter, Adrienne, 14. Their bodies were found buried outside the Mayes' home a week after they were reported missing by Jo Ann Bain's husband, Gary.
Mayes' mother-in-law earlier said she believed Mayes killed the girls' mother and her eldest daughter, and then ran away with the the two girls because he believed the girls were his own children, ABC News reported.
Josie Tate, the mother of Mayes' wife Teresa, told ABC News affiliate WTVC that her daughter and Mayes fought often over whether Mayes was actually the father of JoAnn Bain's two youngest children.
Jo Ann and Adrienne Bain were killed in their Tennessee home on April 27, and then taken with the two youngest daughters to Mayes' home in Mississippi, according to police affidavits.
State and local law enforcement agents searched for Mayes on Thursday in a densely wooded area about 10 miles from Mayes' home near Guntown, Miss. State troopers blocked a road, stopped vehicles and searched their trunks.
Authorities said Mayes had changed his appearance since the mother and children were reported missing. They released surveillance video of him with short hair at a market near Guntown.