New York State Police said they identified an individual as being in the area of the Moreau Lake State Park around the time the girl went missing.
A break in the case came around 4:20 a.m. Monday morning, when a car pulled up to the home of Sena's family and placed a ransom note in the mailbox.
State police immediately began to look for a match with a fingerprint found on the letter. A match was found around 2:30 p.m. linking the fingerprint to a 1999 DWI arrest.
It led police to a house where the suspect's mother was found. They found the suspect, 47-year-old Craig Nelson Ross Jr., in a camper behind the home.
He was taken into custody. New York Gov. Kathy Hochul said charges have yet to be filed against him, but they are expected.
The child was immediately found in a cupboard, both safe and in "good health." She was taken to a local hospital and reunited with family.
"This investigation is a culmination of multiple agencies working together for the common goal of bringing this child home to her loving family," New York State Police said in a statement. "We cannot emphasize enough how appreciative we are for the support we received from Charlotte's community, friends and family."
"We are overjoyed at the news that Charlotte Sena has been located safely this evening after an intense days-long search," New York Gov. Kathy Hochul said in a statement. "Our hearts are with her family as they welcome her home. Thank you to the New York State Police, New York Park Police and all who worked so tirelessly to find Charlotte. It is because of their efforts that Charlotte will be able to return home safe to her family."
The events unfolded when law enforcement officials first issued the Amber Alert Sunday morning after an exhaustive search for Sena because "it was quite possible that an abduction had taken place," state police Lt. Colonel Richard Mazzone said."
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Before she was located on Monday, Sena was last seen riding a bike with friends on Saturday evening in Moreau Lake State Park.
Sena had been riding her bike around a loop in the park with other children when she decided to ride around one more time by herself. Her parents became alarmed when the fourth-grader failed to come back after 15 minutes, Gov. Kathy Hochul said at a briefing Sunday.
The girl's mother called 911 to report her daughter missing after her bicycle was found about 6:45 p.m. Saturday.
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About 400 people took part in the search Monday, up from more than 100 the day before, state police said. The searchers included state and local police, forest rangers, local volunteer firefighters, and some private search and rescue groups, officials said. Authorities also requested help from the FBI.
The search expanded over 46 linear miles by Monday, state police said.
Troopers set up several checkpoints on the rural roads around the park. They stopped drivers and asked if they knew the family, had seen the girl's photo or had any other information. They also had some drivers open their trunks.
Federal authorities also issued a temporary flight restriction over the park for the safety of law enforcement air operations.
"We are leaving no stone, no branch, no table, no cabin unturned, untouched, unexamined in our search to find Charlotte," said Hochul, who described her as a "joyful" girl who was recently elected a class officer for student council.
This story will be updated as more information becomes available.
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ABC News and the Associated Press contributed to this report.