Some people say yes, some say no. There is a difference but it's hard to describe. The way the Native American flute is made will, in my opinion have a much greater effect on the sound it makes than the wood it is made of. Even flutes made of the same wood out of the same board can have markedly different voices. With a metal concert flute the difference in sound quality depends more on the player than the flute. And, all these flutes sound basically alike. With a Native American style flute each flute has its own unique voice. I think that's part of the reason that people start collecting. For more detailed information on wood type and tonal quality go to the page Wood Type, Flute Design and Tonal Quality
Does the type of wood that the Native American flute is made from affect the sound?