A means of making a living both pearls and food, that has been passed down for generations, the canoe that Kino uses represents his link to cultural tradition.
The canoe's symbolism goes beyond its ability to provide sustenance and even beyond the link to Kino's heritage. When the boat is destroyed by the greed that the pearl has caused, it indicates the break between Kino's past and the future he has chosen by refusing to give up the evil object.
