Fairy shrimps (Anostraca) constitute an important component of seasonally aquatic habitats, but few complete mitochondrial genomes have been published for this group. Here, we report the mitogenome of a common southern African species, Streptocephalus cafer, from Botswana (accession number: MN720104). Low-coverage shotgun sequencing recovered two contigs 15653 bp and 1347 bp in length that are separated by a repetitive region of unknown length within the non-coding control region. The mitogenome’s GC content is 31.80%. Phylogenetic analysis using protein-coding genes confirms the sister taxon relationship of S. cafer with the only other congener whose mitogenome has been reconstructed to date, the Asian S. sirindhornae.