Chalcopteryx rutilans Rambur, 1842 (Polythoridae, Odonata) is a species widely distributed in central Amazonia. Due to its sensitivity to environmental changes, it is a bioindicator species used to evaluate the environmental conditions of streams in federally protected areas. By sequencing C. rutilans mitogenome, we report the first whole mitogenome from the Polythoridae family and the first from an Odonata species endemic to South America. The entire mitogenome has 15,653 bp and contains 13 protein-coding, 22 tRNA, and two rRNA genes. The nucleotide composition of the mitogenome is 42.7%, T: 25.5%, C: 19.4%, and G: 12.4%. The AT and GC skews of the mitogenome sequence were 0.249 and −0.220, respectively. C. rutilans was recovered as a sister to Pseudolestes mirabilis Kirby, 1900 (Pseudolestidae), demonstrating the absence of mitogenomes of species from multiple families in the current literature. Mitogenome data from this study will provide useful information for further studies on the phylogeny and conservation of Polythoridae.