John Baugher, the children's father, was arrested shortly after noon in Idaho Springs, Colo., while the three were traveling on a Greyhound bus.
Law enforcement officers boarded the bus about 35 miles outside Denver after it developed mechanical problems and stopped on the side of the highway, said Laura Laughlin, Seattle FBI special agent in charge. The bus was bound from Salt Lake City to Hartford, Conn., via Denver, she said.
The FBI was reuniting the children -- 4-year-old Remi Baugher and her 2-year-old brother, Lars -- with their mother, said Agent Larry Carr.
John Baugher, 34, was charged Monday in Walla Walla County Superior Court with custodial interference for failing to return the children to their mother after a visit. A warrant was issued for his arrest. He was held at the Clear Creek County Jail pending his return to Washington.
The Amber Alert was issued in Walla Walla for the children on Sunday. Baugher's van was found Monday in northeast Washington and the father and children were seen Tuesday at a fast-food restaurant and a department store in Missoula, Mont., where they were taped on surveillance cameras. He also was spotted Wednesday evening at a Salt Lake City bus station.
The FBI said it appeared that Baugher altered the appearance of the children, cutting Remi's hair short and dressing her like a boy, and dyeing both children's hair darker.
Officials had said they were concerned for the children because Baugher has mental health problems.