Abstract: The complete mitochondrial genome (mtDNA) of snow leopard Panthera uncia was obtained by using the polymerase chain reaction (PCR) technique based on the PCR fragments of 30 primers we designed. The entire mtDNA sequence was 16 773 base pairs (bp) in length, and the base composition was: A-5,357ª“,Ž+bp (31.9%); C-4,444ª”,Ž+bp (26.5%); G-2,428ª“,Ž+bp (14.5%); T-4,544ª”,Ž+bp (27.1%). The structural characteristics [0] of the P. uncia mitochondrial genome were highly similar to these of Felis catus, Acinonyx jubatus, Neofelis nebulosa and other mammals. However, we found several distinctive features of the mitochondrial genome of Panthera unica. First, the termination codon of COIII was TAA, which differed from those of F. catus, A. jubatus and N. nebulosa. Second, tRNASer (AGY), which lacked the ''DHU'' arm, could not be folded into the typical cloverleaf-shaped structure. Third, in the control region, a long repetitive sequence in RS-2 (32ª“,Ž+bp) region was found with 2 repeats while one short repetitive segment (9ª”,Ž+bp) was found with 15 repeats in the RS-3 region. We performed phylogenetic analysis based on a 3 816ª",Ž+bp concatenated sequence of 12S rRNA, 16S rRNA, ND2, ND4, ND5, Cyt b and ATP8 for P. uncia and other related species, the result indicated that P. uncia and P. leo were the sister species, which was different from the previous findings. (c) 2008 Springer Science+Business Media B.V.