Robert Faison, 45, of West Haven, had disappeared after his 42-year-old wife, Lindsey Hopkins, was found dead inside her home in Guilford on July 22, police said.
She had suffered blunt trauma injuries to her head and neck and her death was ruled a homicide.
About a week later on July 30, Faison was found living at the New York shelter and has been in custody since being extradited to Connecticut in August on an outstanding violation of a probation warrant.
Court records show the couple had filed for divorce but later called off those proceedings. Guilford Police Chief Warren "Butch" Hyatt told the Hartford Courant that although the couple had been separated and planned to divorce, they ended up reconciling and getting back together.
The Courant reported that Faison has a history of domestic violence offenses, but it was not clear if Hopkins was a victim in any prior cases. Hyatt said he believed the previous arrests involved other women.
The murder charge was added Thursday and a judge ordered Faison held in lieu of a $2 million bond.
Faison's attorney, a public defender in Waterbury, did not immediately respond to an email seeking comment.
WATCH FOX 5 NEWS: