| Summary: | <i>Hyphessobrycon heterorhabdus</i> (Ulrey, 1894), popularly known as ‘Flag Tetra’ in English speaking countries, belongs to the genus <i>Hyphessobrycon</i> of the family Characidae, and is widely present in the eastern Amazon basin. Here, using Illumina sequencing, we report the complete mitogenome sequence of <i>H. heterorhabdus</i>. Overall, the mitogenome has 17,021 bp, containing 13 protein-coding, 22 tRNA, and 2 rRNA genes. Non-ambiguous nucleotide compositions of the <i>H. heterorhabdus</i> mitogenome are A: 29.2%, T: 29.4%, G: 15.6%, and C: 25.8%. As recently indicated, the phylogenetic analyses did not support four separate genera (<i>Hemigrammus</i>, <i>Hyphessobrycon</i>, <i>Moenkhausia</i>, and <i>Psalidodon</i>) of Characidae. Understanding the <i>H. heterorhabdus</i> mitogenome is important for taxonomic purposes as well as for the molecular characterization of environmental pollutants. Thus, the mitogenome described here will be a valuable resource for studies on environmental changes, evolutionary genetics, species delimitation, and phylogenetic analyses in Characidae.
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