Kay Lynn Jackson, 22, was found dead along the Boise Greenbelt 15 years ago on April 5, 1998.
BPD said Wednesday that first degree murder and rape charges were filed against Patrick Jon Zacharias, who's already serving a life sentence in prison for lewd conduct with a minor under the age of 16.
Jackson was walking to church along the Greenbelt carrying a Bible in her hands. Her body was found in a tunnel under the Americana Boulevard bridge.
"We all have been waiting 15 years for this day," said Pete Ritter, Boise Police deputy chief. "I'm very pleased to be able to tell you that after 15 years, more than 1,000 leads and hundreds of hours put in by detectives, charges have been filed in the murder of Kay Lynn Jackson."
Zacharias has been in prison since February of 2007.
"Her faith in God has kept us going all these years," family members said in a prepared statement Wednesday.
Zacharias was denied bail Wednesday in court, although it didn't really matter as he's serving a life sentence. He was also provided a public defender.
During his incarceration, a sample of Zacharias' DNA was taken and entered into a national crime information database, which led to a major break in this case, BPD said.
"We just try to keep her memory in our hearts," Kathleen Jackson, Kay Lynn's sister, told KBOI-TV in a 2009 investigation.
Boise Police Det. Mark Ayotte has worked on the case from the beginning.
"That day began 15 years of investigation that have had moments of promise and moments of frustration," Ritter said. "Det. Ayotte pursued leads that went throughout Idaho and the world."