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We used next-generation methods to sequence the mitochondrial genome of Allonautilus scrobiculatus from two large, overlapping amplicons generated by PCR. The genome was circular, 16,132 base pairs in length, and possessed the same sequence and orientation of genes as the previously sequenced mitogenome of Nautilus macromphalus. These two mitogenomes were approximately 8% divergent overall, but differentiation varied greatly among genes: some tRNA sequences were identical between the two taxa, whereas ATP8 differed by over 15%. The largest of the noncoding regions of the genome included a 62 base pair repeat that was essentially identical between the two genera; however, this repeat was present as six copies in N. macromphalus, but varied between four and five among individuals of Allonautilus. A 146 base pair deletion (in Allonautilus compared to Nautilus) included one copy of the repeat plus an adjacent 84 bp; because of this indel, the “CA” microsatellite in N. macromphalus was missing from Allonautilus. Base composition varied along the Allonautilus sequence, and was correlated with the strand on which genes coded. Base composition also varied within the largest noncoding region. A phylogeny of 24 extant cephalopods indicates that there is less molecular divergence between Allonautilus and Nautilus than there is among congeneric species of Octopus and Sepia.