The purpose of this study was to identify the wood species of the marine and filling piles obtained from the ancient Byzantine port of Eleutherius/Theodosius, Istanbul, Turkey. Anatomical descriptions and identifications of 12 marine and 4 filling piles were performed by microscopic evaluations. In the study, Castanea sativa Mill., Quercus ithaburensis Decne., Quercus pontica C. Koch., and Cupressus sempervirens L. species were identified. No precise identifications were completed for only six samples at the species level; however, those samples showed significant similarity to Quercus spp. and Fagus spp. It was concluded that the economically viable supply of wood was more appropriate than obtaining it from nearby regions. The people living in ancient times had solid knowledge and experience on the utilization of wood species.