His wife, Lisa Clark, was charged with hindering the apprehension of a child, said Douglas County Sheriff Phil Miller. She is expecting the teenager's baby in about a week.
Richard Mecum of the U.S. Marshals Service said authorities tracked the boy to a residence in Cleveland through a package Clark mailed. The package contained a cell phone and money.
Posing as a delivery man, a deputy dropped the package off at the home and was able to determine that the boy was living there, authorities said. Mecum said the residents did not know he was a runaway.
Clark, in the Douglas County Jail, had no role in his disappearance and had no idea where he was, Clark's attorney, Dan Sammons, said last week.
The two married in November. Clark, previously charged with child molestation, was released on bond on the condition that she not have contact with the teen.
Clark has said she still hopes to make a life with the child groom and their baby.