The complete mitochondrial genome of <i>Cyphocaris challengeri</i> (Amphipoda: Cyphocarididae)

The amphipod <i>Cyphocaris challengeri</i> is a globally distributed, highly abundant species of zooplankton. Here, we report the complete mitochondrial genome of <i>C. challengeri</i> obtained using the Illumina sequencing platform from a specimen collected from Puget Sound, Washington. The mitogenome is a circular DNA molecule with a size of 14,338 bp and 26.7% GC content, with 13 protein-encoding genes, 2 rRNAs, and 22 tRNAs annotated. A maximum likelihood phylogenetic analysis including <i>C. challengeri</i> and all other available mitogenomes from Amphipoda places our mitogenome firmly within the Lysianassoidea superfamily, as expected. The newly described mitochondrial genome of <i>C. challengeri</i> fills a gap in valuable reference data for detecting this organism using molecular methods such as environmental DNA.