For visual inspection-based wood identification, optical microscopy techniques typically require a relatively large sample size, and a scanning electron microscope requires a clean surface. These novel techniques experience limitations for objects with highly limited sampling capabilities such as important and registered wooden cultural properties. Synchrotron X-ray microtomography (SR-μCT) has been suggested as an effective alternative to avoid such limitations and various other imaging issues. In this study, four pieces of wood fragments from wooden members used in the Manseru pavilion of Bongjeongsa temple in Andong, Korea, wereused for identification. Three-dimensional microstructural images were reconstructed from these small wood samples using SR-μCT at SPring-8. From the analysis of the reconstructed images, the samples were identified as Zelkova serrata, Quercus sect. Cerris, and Pinus koraiensis. The images displayed sufficient spatial resolution to clearly observe the anatomical features of each species. In addition, the three-dimensional imaging allowed unlimited image processing.