The 49ers head coach told The Plain Dealer: "[Smith is] an excellent football player. He's really playing the best football of his career the last two years. We think we've got the best quarterback situation in the National Football League.
"Again, that will be a process that plays out, I mean Alex Smith continuing to be a 49er, or if a trade occurs in the next weeks or months, those are the two most likely possibilities."
Smith has been linked to the Kansas City Chiefs and Arizona Cardinals.