The dung beetle, Copris tripartitus, has been listed as an endangered insect in Korea. In contrast to typical genomic characteristics, the 15,457-bp long, the complete mitochondrial genome (mitogenome) of C. tripartitus has a few unusual characteristics. The genome has the trnP-trnT arrangement at the ND4L-ND6 junction, which is found only in two species of Scarabaeoidea, including C. tripartitus, in 53 available species. Twelve protein coding genes (PCGs) have typical ATT and ATG start codons, whereas COII had the start codon GTA, which is unprecedented in Scarabaeidae. The 297-bp A + T-rich region, which is the shortest available in Scarabaeidae, harbors three repeat units (26, 29, and 21 bp), each consisting of duplicated identical sequences interspersed in the A + T-rich region. Phylogenetic analyses were performed using the concatenated sequences of the 13 PCGs and two rRNA genes using both the Bayesian inference (BI) and maximum likelihood (ML) methods for the families Scarabaeidae and Lucanidae that are available for their mitogenomes in Scarabaeoidea. Our consensus phylogeny yielded monophylies of each family and the subfamily Scarabaeinae in Scarabaeidae with the high nodal supports (0.99-1 by BI and 79-100 by ML). Among the three tribes, represented by multiple genera in Scarabaeinae each Oniticellini and Onitini was supported as monophyletic groups with the highest nodal supports (1 by BI and 100 by ML), whereas Onthophagini was non-monophyletic group, presenting the tribe relationships: ((((Oniticellini + Onthophagini [Caccobius, Milichus, Onthophagus]) + Onthophagini [Digitonthophagus, Phalops]) + Onitini) + (Phanaeini + Eurysternini) + Coprini).