The tadpole shrimp (Notostraca: Triops) have been called living fossils with conserved morphology, but subtle morphological variations within and between species has yielded confused taxonomic assignments. To aid in cryptic species detection of tadpole shrimp from southern New Mexico, USA, the first complete mitochondrial genomes for three putative species (T. longicaudatus “long,” T. l. “short,” T. newberryi) are reported. The genomes ranged in length from 15,058 bp to 15,060 bp with 13 coding genes, 22 tRNA genes, 2 rRNA genes and a control region. Phylogenetic trees were constructed using previously sequenced Triops-genomes to assess genetic relationships within the genus. The T. longicaudatus-genomes from Genbank were consistent with our genomes for T. newberryi and T. l. “short.” Variation in mitochondrial genes were identified that will aid future identification of cryptic lineages of tadpole shrimp. Genetic differentiation among the genomes of Triops in New Mexico support elevation to species status.