Stephen Howells and Nicole Vaisey of Hermon were each charged Friday with two counts of first-degree kidnapping.
St. Lawrence County District Attorney Mary Rain said 39-year-old Howells and 25-year-old Vaisey were jailed without bond.
The sisters, ages 7 and 12, vanished Wednesday night in Oswegatchie, touching off a massive search in the farming community near the Canadian border. They turned up safe Thursday night at the door of a house 15 miles from where they were taken. The Associated Press generally does not identify victims of alleged sexual abuse.
Rain declined to discuss a motive for the abduction or provide any other specifics about the suspects. She said information provided by the girls helped lead to Howells and Vaisey. The suspects' home is about 13 miles from where the girls live.
"The suspects agreed to go to the sheriff's office to be interviewed earlier today and they were arrested after those interviews," Rain said.
Searchers had scoured the farming community of about 4,000 people, in a hunt hampered by a lack of photos of the girls for authorities to circulate.
The Amish typically avoid modern technology, and the family had to work with an artist who spoke their language, a German dialect known as Pennsylvania Dutch, to produce a sketch of the older girl.
The episode left a sense of vulnerability in a community where residents said even small children often walk unaccompanied to school.
"One thing that comes from this is that people learn this can happen in a small town," the prosecutor said. "I think the public will take precautions, and that's the sad thing."
Patricia Ritchie, the state senator representing the region, said many are now reluctant to let their children play outdoors unattended.
Ritchie said the Amish are responding in a way that may forever change a familiar feature of the local landscape: Some are taking down their roadside stands.
"This has sent a shockwave through their community," she said.