Craig Nelson Ross Jr., 46, was arraigned and charged with first-degree kidnapping. He's being held at Saratoga County jail without bail and more charges are expected to be filed against him.
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New York State Police said they identified him 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 the girl'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. Monday linking the fingerprint to a 1999 DWI arrest in Saratoga.
It led police to a house where the suspect's mother was found. They found the suspect in a camper behind the home and he was taken into custody.
"After some resistance, the suspect was taken into custody and immediately the little girl was found in a cabinet," Gov. Kathy Hochul said. "She knew she was being rescued. She knew that she was in safe hands."
She was taken to a local hospital and reunited with her family.
How do you talk to your children about kidnapping?
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"We are thrilled that she is home and we understand that the outcome is not what every family gets," her family said in a statement Tuesday. "A huge thank you to the FBI, the New York State Police, all of the agencies that were mobilized all of the families, friends, volunteers."
The road leading up to the site where the girl was rescued was no longer blocked off as of Tuesday morning. The property owned by the suspect's mother, adorned with Halloween decorations, was lined with yellow tape. It was not immediately clear if anyone was home.
Investigators with the police, dressed in hazmat suits, could be seen walking into the suspect's mother's home, as well as a white trailer located at the side of the house.
Before she was located on Monday, the girl was last seen riding a bike with friends on Saturday evening in Moreau Lake State Park, about 35 miles north of Albany.
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 and state police issued an Amber Alert.
More than 400 people including state and local police, forest rangers, local volunteer firefighters, and some private search and rescue groups took part in the search for the girl.
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ABC News and the Associated Press contributed to this report.
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