Craig Nelson Ross Jr., 47 was arraigned and charged with first-degree kidnapping. He's being held at Saratoga County jail without bail.
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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 , 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, Ross Jr., in a camper behind the home.
He was taken into custody.
The girl was immediately found in a cupboard, both safe and in "good health." She was taken to a local hospital and reunited with her family.
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"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 are overjoyed at the news that she 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 her. It is because of their efforts that she will be able to return home safe to her family."
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.
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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This story will be updated as more information becomes available.
ABC News and the Associated Press contributed to this report.