We sequenced the complete mitochondrial (mt) genome of the kisslip cuttlefish, Sepia lycidas, made the comparison with the mt genomes of other cuttlefishes, and constructed phylogenetic trees estimating their relationships. The genome was 16,228 bp and contained 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and 2 long-noncoding regions [both in the control regions (CR)]. The composition and order of genes in S. lycidas were similar to those of most other invertebrates. The overall base composition of S. lycidas is 35.8% T, 14.8% C, 41.3% A, and 8.1% G, with extremely high A+T content (77.1%). Both control regions contain termination-associated sequences and conserved sequence blocks. Maximum likelihood and Bayesian methods were used to build phylogenetic trees based on protein coding mtDNA genes of 37 cuttlefish species. S. lycidas have a close relationship with S. pharaonis, S. aculeata, and S. esculenta. This result confirmed the relationships of S. lycidas as being similar to the traditional taxonomy. This study plays an important role in the investigation of phylogenetic relationships, taxonomic resolution, and phylogeography for Sepiidae species.