The complete mitochondrial DNA sequence of the frigate tuna Auxis thazard and two divergent mitotypes (Mitotype I and Mitotype II) of the bullet tuna Auxis rochei have been determined. The total length of the mitogenomes was 16,506, 16,501 and 16,503 bp, respectively. All mitogenomes had a gene content (13 protein-coding, 2 rRNAs and 22 tRNAs) and organization similar to those observed in most other vertebrates. The major non-coding region (control region) ranged between 843 and 847 bp in length, and showed the typical conserved blocks. Phylogenetic analyses revealed a monophyletic origin of Auxis with respect to other tuna fish. Molecular data here presented provide a useful tool for evolutionary as well as population genetic studies.