In 2008, a medieval wooden shipwreck was discovered at the port of Rhodes, Greece. The shipwreck was party burned, presenting a challenge for conservators, as uncharred, semi-charred and charred waterlogged wood were often encountered on the same piece of timber. In seeking the most appropriate conservation method for this unusual material, its chemical characterization was considered necessary. This study examined the chemistry of the three dominant wood conditions found in the wreck. Fourier transform infrared spectroscopy and X-ray diffraction analysis were implemented in comparison to reference samples. Energy dispersive analysis was also used for assessing the inorganic composition of each condition. Moreover, for charred and semi-charred wood, proximate analysis was undertaken. Results obtained regarding the organic moieties of the waterlogged archaeological material, demonstrated that charred samples were chemically comparable to charcoals, semi-charred material showed similarity to thermally modified wood, whereas uncharred waterlogged wood was proven to have an analogous chemistry to biodeteriorated wood. Elemental analysis results also diversified among the three shipwreck’s conditions. Sulfur, iron, and oxygen decreased in charred areas, whereas carbon increased. Proximate analysis showed that ash and fixed carbon content increased with charring, whereas volatile mater decreased. This work proved major chemical differences among shipwreck timbers’ conditions owing to different degree of charring. These are anticipated to influence not only conservation methods’ efficacy, but also the post-treatment behavior of the material. Further investigation is needed for correlating the chemistry of the archaeological material to its physical properties in order to contribute to practical aspects of conservation.