Noah Cownden was found dead on April 9, 2008.
His death was initially deemed suspicious, but police said later they were no longer involved in the case because there were no criminal aspects.
However, the Vancouver Island Integrated Major Crime Unit announced on Monday that 29-year-old Bradley Streiling has been charged with second degree murder.
Police are not commenting on any specifics of the case, including Streiling's relationship with the toddler.
The cause of death is also not known. (CFAX)