Deputy Prosecutor Rachael Probstfeld filed two counts of unlawful imprisonment-domestic violence on Monday against the boys' father, 30-year-old John Eckhart and his 26-year-old girlfriend, Alayna Higdon.
Police say the boys - ages 5 and 7 - were found April 12 in the couple's apartment in a room with a metal slatted cage-like door. Police say the boys shared a single mattress, were wearing diapers and were not enrolled in school.
The Columbian says the maximum penalty for the charge is five years and the minimum is one to three months.
Eckhart and Higdon will be arraigned April 27. Their lawyers have not commented.
The boys have been placed in state care, as have two other children who lived in the apartment.