The high economic value and increased demand for timber have led to illegal logging and overexploitation, threatening wild populations. In this context, there is an urgent need to develop effective and accurate forensic tools for identifying endangered Guibourtia timber species to protect forest ecosystem resources and regulate their trade. In this study, a hybridization capture method was developed and applied to explore the feasibility of retrieving complete plastid genomes from Guibourtia sapwood and heartwood specimens stored in a xylarium (wood collection). We then carried out forensic identification and phylogenetic analyses of Guibourtia within the subfamily Detarioideae. This study is the first to successfully retrieve high-quality plastid genomes from xylarium specimens, with 76.95–99.97% coverage. The enrichment efficiency, sequence depth, and coverage of plastid genomes from sapwood were 16.73 times, 70.47 times and 1.14 times higher, respectively, than those from heartwood. Although the DNA capture efficiency of heartwood was lower than that of sapwood, the hybridization capture method used in this study is still suitable for heartwood DNA analysis. Based on the complete plastid genome, we identified six endangered or commonly traded Guibourtia woods at the species level. This technique also has the potential for geographical traceability, especially for Guibourtia demeusei and Guibourtia ehie. Meanwhile, Bayesian phylogenetic analysis suggested that these six Guibourtia species diverged from closely related species within the subfamily Detarioideae ca. 18 Ma during the Miocene. The DNA reference database established based on the xylarium specimens provides admissible evidence for diversity conservation and evolutionary analyses of endangered Guibourtia species.

木材的高经济价值和不断增长的需求导致了非法采伐和过度开发，威胁着野生种群。在此背景下，迫切需要开发有效、准确的法医工具来识别濒临灭绝的吉布提亚木材物种，以保护森林生态系统资源并规范其贸易。在本研究中，开发并应用了一种杂交捕获方法，以探索从储存在 xylarium（木材收藏）中的Guibourtia边材和心材标本中检索完整质体基因组的可行性。然后，我们对 Detarioideae 亚科的Guibourtia进行了法医鉴定和系统发育分析。这项研究首次成功地从木质素样本中检索出高质量的质体基因组，覆盖率达到 76.95-99.97%。边材质体基因组的富集效率、序列深度和覆盖度分别是心材的16.73倍、70.47倍和1.14倍。虽然心材的DNA捕获效率低于边材，但本研究采用的杂交捕获方法仍然适用于心材DNA分析。基于完整的质体基因组，我们在物种水平上鉴定了六种濒临灭绝或经常交易的Guibourtia木材。该技术还具有地理可追溯性的潜力，特别是对于Guibourtia demeusei和Guibourtia ehie。同时，贝叶斯系统发育分析表明，这六个Guibourtia物种与 Detarioideae 亚科中密切相关的物种分化。18 Ma，中新世。基于木质素标本建立的DNA参考数据库为濒危吉布氏菌多样性保护和进化分析提供了可采的证据。