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We sequenced a complete mitochondrial genome of the marine sponge, Cacospongia mycofijiensis, which is the first report for the family Thorectidae in the class Demospongiae. The mitogenome was obtained from a de novo assembly of shotgun genome sequencing using Illumina Miseq technology, which reconstructed a circular genome with 97 × of sequence coverage. The assembled mitochondrial genome consisting of 16,227 bp includes 14 protein-coding genes, 2 rRNAs and 2 tRNAs. This complete mitogenome sequence will be useful especially for the phylogenic studies of Demospongiae.