Leopards, as the most widely distributed felids, remain phylogeographically understudied due to sampling gaps across its vast range distribution. In this study, we assembled the most comprehensive genomic dataset to date, spanning all the subspecies (n=198 from archival tissues, field collections and published data). Mitochondrial genomes resolve seven Asian subspecies plus three African haplogroups (West, Central and South), while nuclear genomes reveal admixtures with weak structure (FST <0.05) highlighting 30-75% of mito-nuclear discordance likely driven by ILS. Moreover, we identify in Africa a Congo Basin diversity hotspot (Par II) and three sub-Saharan lineages (Par I, II and III). These data can be further used as a genomic reference baseline, enabling forensics to trace origin of illegal trade of leopard body parts seizures (e.g. for the west African haplogroup). This is critical as leopards face 70% historical range loss and escalating CITES Appendix I seizures. Thus, resolving marker-type discrepancies is essential for effective conservation action plans particularly when facing ongoing species decline.