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The structure and composition of the mitogenome of a bivalve mollusk, denoted as Mactra sp. (MT780813), has been obtained. The genome has a variable organization: it includes 12 protein-coding genes, 28 tRNAs, and two rRNA genes. Its content is sufficiently different from that of nearest specimen, accessed from GenBank, supposedly belonging to the other gender. All genes are encoded on the “+”-strand. All protein-coding genes are initiated with ATG codon. Analysis confirms the close topological position of the GenBank Mactra chinensis (KJ754823) and our M. sp. specimen on gene tree. Above data suggesting female- vs. male-type mitogenomes or cryptic species presence.