Acropora nana belongs to Cnidaria phylum, Anthozoa class, and staghorn coral groups. Like other corals, Acropora could be an indicator for environmental changes and with great conservational values. In this study, the complete mitogenome sequence of A. nana (Cnidarian: Acroporidae), has been decoded for the first time by low coverage whole genome sequencing method. The overall base composition of A. nana mitogenome is 25.0% for A, 13.8% for C, 24.4% for G, and 36.9% for T, and has low GC content of 38.2%. The assembled mitogenome, consisting of 18,480 bp, has unique 13 protein-coding genes (PCGs), three transfer RNAs, and two ribosomal RNAs genes. The A. nana has one big intron insert in ND5 gene. The complete mitogenome of A. nana provides essential and important DNA molecular data for further phylogenetic and evolutionary analysis for stony corals.