Species sequenced in this study.

Effective conservation of wild mammals necessitates accurate taxonomic classification and reliable genetic reference data. In China, the List of State Key Protected Wild Animals serves as a critical tool for species protection. However, taxonomic revisions and gaps in genetic data can impede its effectiveness. In this study, we updated the List of State Key Protected Wild Animals (2021) by incorporating recent taxonomic and distributional evidence, resulting in a refined list of 169 mammalian species that are protected. We identified 15 taxa lacking complete mitochondrial genome data and addressed this gap by generating 12 new mitogenomes for nine taxa using a combination of GenBank database mining and next-generation sequencing of museum specimens and fecal samples. These efforts led to the establishment of a curated mitochondrial genome reference database encompassing 164 species. Our analyses also uncovered taxonomic ambiguities in genera such as Moschus and Naemorhedus, and highlighted mislabeling issues within public genetic databases. This curated database enhances the accuracy of forensic species identification, supports biodiversity monitoring, and strengthens wildlife law enforcement. Our findings underscore the value of integrating historical specimens with mitogenomic approaches to advance wildlife conservation efforts.