Whole mitochondrial genome sequences have important applications for phylogenetic inference, population evolution, and population structure. In this study, we sequenced the entire mitochondrial genome of a sun bear (Helarctos malayanus) from Peninsular (West) Malaysia using Illumina Miseq technology and used 26 additional mitochondrial genomes from the Ursidae, including 5 sun bears, to generate a phylogeny. The complete mitochondrial genome of the sun bear consisted of 16,770 base pairs (bp), including 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs, and a noncoding, adenine–thymine (AT) -rich control region. Maximum likelihood and Bayesian inference phylogenetic trees revealed topologies identical to trees previously published using whole mitochondrial genomes. Sun bears formed 2 distinct mitochondrial lineages, with the peninsular genome occupying a clade separate from the clade including a sun bear from Yunnan, China. Within the control region, all 5 sun bear genomes differed at a microsatellite repeat region and all 5 genomes consistently lacked a 6-bp imperfect repeat, which is found in some bear species. Ursine phylogenies constructed with whole mitochondrial genomes conflict with recent well-resolved coalescent trees employing whole genome data. However, both phylogenies suggest a historical split in the sun bear lineage. Furthermore, the inclusion of the peninsular sun bear mitochondrial genome suggests that this split does not conform to the current subspecies delineation in sun bears. Genomic data from multiple individuals of known geographic origin will help to resolve this question.