St. Lawrence County's District Attorney Mary Rain says 39-year-old Stephen Howells and 25-year-old Nicole Vaisey of Hermon were each charged Friday with two counts each of first-degree kidnapping.
She says they're in custody awaiting arraignment Friday night and additional charges are possible.
The sisters vanished Wednesday evening in Oswegatchie (ahs-wee-GAH'-chee), 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 their home.
The episode has 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," Rain said. "I think the public will take precautions, and that's the sad thing."
Patricia Ritchie, the state senator representing the region, 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.
Word of the girls' return came shortly after about 200 people attended a candlelight prayer vigil at Cornerstone Wesleyan Church in nearby Heuvelton. Dot Simmons, a member of the congregation and neighbor of the Miller family, said despair turned to joy when she returned home from the vigil to word that the girls were safe.
Authorities initially said the sisters vanished at about 7:30 p.m. Wednesday after a light-colored car pulled up to the farm stand and they went down to tend to the customers while the rest of their family stayed at a barn for the evening milking. By Thursday night, however, they were looking for a red car.
Searchers had scoured Oswegatchie, a farming community of about 4,000 people about 150 miles north of Albany, 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 girls are among the youngest of Mose and Barb Miller's 13 children, who range in age from 1 to 21 years, said Simmons. The girls routinely took on the chore of selling the fruits, vegetables, jams and other products of the farm, Simmons said.