Clam shrimps (Spinicaudata) are a widespread and diverse crustacean group that frequent temporary aquatic habitats, but few complete mitochondrial genomes have been published for this group. Here, we report the mitogenome of an undescribed Gondwanalimnadia species from Botswana. Raw sequences were assembled into a single circular genome with a total length of 15,663 bp. Thirteen protein-coding genes, 22 tRNAs, and 2 rRNAs were identified using the MITOS pipeline. The mitogenome’s GC content is 33.52%. Phylogenetic analysis using protein-coding genes confirmed that Gondwanalimnadia sp. is closely related to another member of the Limnadiidae, Limnadia lenticularis.