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The complete mitochondrial genome of a cryptic species of tadpole shrimp from South Africa (Accession Number: MG770893) was recovered by low coverage shotgun sequencing. The mitogenome consists of 15,216 bp with a GC content of 30.95%. COX1 sequence alignment indicates that this specimen is the most closely related to Triops granarius with a pairwise nucleotide identity of less than 90% (86.6%). Phylogenetic analysis using whole mitogenome dataset supports its affiliation to the genus Triops with moderate support for its relatively basal position within the clade. [ABSTRACT FROM AUTHOR]