Raven Abaroa, 30, was arrested at his home in Montpelier, Idaho without incident on Monday.
He was placed in an Idaho jail without bond. He is being held for extradition to North Carolina.
In the hours before her death, Janet Abaroa, who was in the early stages of pregnancy, picked up her 6-month-old son at day care and went with her husband to drop her car off for repairs.
The Abaroas met with a church member at their home that evening before Raven Abaroa left the house around 8:30 p.m. in a gray Dodge Durango to play in an indoor soccer game in Morrisville.
Raven Abaroa told officers he found his wife when he returned home from the game around 11 p.m.
The couple's son, Kaiden, was also at home in the next room, but was not injured.
There were no obvious signs of a break-in, but a laptop computer was missing from the couple's house.
Raven Abaroa moved away after his wife's death and remarried. His second wife later went public after the two separated and said he may have been involved in the murder.
Abaroa's arrest was a joint operation by the Durham Police Department, the FBI Task Force, the North Carolina State Bureau of Investigation, the Montpelier (Idaho) Police Department, the East Idaho STAR (Special Tactics and Response) Team and the Bear Lake County (Idaho) Sheriff's Department.
"This arrest is the result of hard and tenacious work by our investigators and a strong partnership with the FBI and the North Carolina SBI. Investigators continued to follow leads and never gave up," said Durham Police Chief Jose L. Lopez Sr.
Over the past five years, the case has been assigned to four investigators -- Cpl. Bennie Bradley, Cpl. Steve Vaughan, Investigator Charles Sole and Sgt. Sheldon Perkins.
"Although an arrest has been made, the case is still ongoing and investigators continue to gather information and conduct interviews," Lopez said. The chief said he can't comment further on the case because the investigation is still ongoing and has not yet been adjudicated.
"We do not give up on our homicides. We continue to follow up until all leads are exhausted and then we check out any new leads we receive," Lopez said.
Anyone with further information on this case is asked to contact Investigator Sole at (919) 560-4440, ext. 29350 or by email at Charles.Sole@durhamnc.gov. or Sgt. Perkins at (919) 560-4440, ext. 29326 or by email at Sheldon.Perkins@durhamnc.gov .