He told a judge he understood his rights as well as the charges against him.
The 40 year old is charged with raping and stabbing Kay Lynn Jackson to death on the Boise Greenbelt in 1998.
He was formally arraigned on those charges Friday and is scheduled to enter a plea May 17.
Prosecutors say they have not yet determined if they are going to seek the death penalty.
Zacharias is already serving a life sentence at the Idaho Correctional Center south of Boise after a 2007 conviction for lewd conduct with a minor.
Police announced this week he has been linked to Kay Lynn Jackson's murder through DNA testing.
Jackson, 22, was murdered on the Greenbelt as she walked to church on Palm Sunday 1998, a crime that shocked the community and contributed to years of uncertainty.
Jackson was the first of three women murdered on the Greenbelt in a three-year-period.