The remains of Myrna Letandre were found in May 2013 in a Winnipeg home.
She was reported missing by her sister in October 2006.
Investigators with the RCMP and Winnipeg police arrested Traigo Andretti in British Columbia and have charged him with second-degree murder.
Police say the 38-year-old, who was convicted in the first-degree murder of his wife in British Columbia in April, was being brought back to Winnipeg.
"Our investigators ... worked in a unified approach with the Vancouver integrated homicide unit and in order to allow them to complete their investigation we waited until such time as that process ... was over and then subsequently got on with our investigation and laid charges," said Winnipeg police Supt. Danny Smyth.
The RCMP recently released a report estimating there have been almost 1,200 cases of missing and murdered aboriginal women since 1980.
Letandre, who was 37, was originally from Pinaymootang (Fairford) First Nation in Manitoba's Interlake area.
In the B.C. case, Andretti admitted to killing and dismembering his wife, Jennifer McPherson, who was also a longtime Winnipeg resident.
Police discovered the scattered remains of McPherson on a remote island near Alert Bay, off the east coast of Vancouver Island, last spring. She had been reported missing from Hanson Island, B.C., on May 1, 2013.
The couple had been living there as caretakers of a remote fishing resort called the Pacific Outback Resort.
Note to readers: This is a corrected story. An earlier version said Andretti was convicted of his wife's murder in May.