Matthew Jones, 44, of Grant and Paul Jones, 42, of Newaygo were arrested and charged in Newaygo County. The death of Shannon Siders, 18, of Newaygo was given more attention by state and local investigators starting in 2011.
"This case remained open for many years, but Shannon Siders was never forgotten and law enforcement's resolve to hold those accountable for her death never diminished," county prosecutor Robert Springstead said in a statement.
The Jones brothers appeared in court and were ordered to jail without bond. It wasn't immediately known if they have lawyers.
Siders disappeared in July 1989. A hunter that fall found her body in the Manistee National Forest.
The body was exhumed from a cemetery in 2012 as part of the investigation.
"I've always been kind of suspicious," said Siders' father, Robert Siders. "The names do not surprise me. She knew them in the circle of friends she hung around with. One of them, I had passed many times in a party store."
A statement announcing the charges from Attorney General Bill Schuette's office didn't indicate why police finally settled on the Jones brothers.