In our study, identification of timber species, based on their microscopic structures, was carried out on 29 samples from different hull units of the Southern Song Dynasty Huaguangjiao Ⅰ shipwreck, including the 1st to the 5th decks, the keel and columns. The results show that timber species were diverse but that the most frequently-used timbers are Cinnamomum Trew, Machilus Nees, Cunninghamia R.Br, Pinus Linn, Cupressus Linn and Drypetes Vahl, which are mainly from the central and southern China. Pinus Linn. is the main species. Most of these timbers are important traditional shipbuilding materials in China. In addition, the characteristics and sources of timbers used for different parts of the ship for different purposes were analyzed. Timber selection of Huaguangjiao Ⅰ shipwreck indicates that ancient craftsmen not only knew well the properties of different timbers, but could also reasonably select timbers for hull units with different functions.