It is not wood that makes petrified wood colorful, but the chemistry of the petrifying groundwater. The silica can be agate, jasper, chalcedony or opal. The beautiful and varied colors of petrified wood are caused by the presence of other minerals that enter the wood in solution with the silica. Iron oxides stain the wood orange, rust, red or yellow. Manganese oxides produce blues, blacks or purple.