Originally from Mattis Point, Carol King was 40 when she disappeared on Aug. 6, 2011.
Police were unable to find any signs of King on her farm near Herschel, but her car was located in a slough a few days later.
Her remains were discovered in a wooded area three weeks after she was reported missing and had to be identified through dental records.
Joseph (David) Caissie of Bluffton, Alta., has been charged with first- degree murder and offering an indignity to human remains.
Police say Caissie, who is 53, was King's former boyfriend.
He was arrested near the SaskTel Centre in Saskatoon and was to appear in provincial court Wednesday.
In a brief written statement, King's family said they have a sense of relief knowing that charges have been laid.
In the weeks after King vanished, dozens of volunteers searched the Herschel area looking for her and candlelight vigils were held in her honour.
In Newfoundland, King's family offered a reward of $25,000 for information on her disappearance. A man driving a quad about 10 kilometers north of Herschel found the remains.
In December 2011, a cryptic memorial for King was set up at an abandoned property near the small community. That same month, her former home in Herschel burned down and the cause was determined to be arson.
An RCMP spokesman said Tuesday that police don't have any information on whether Caissie was connected to the arson.