The Salt Creek pupfish, Cyprinodon salinus salinus Miller, 1943 is endemic to Death Valley, California, USA, and resides as a single population within one of the most extreme inland aquatic environments capable of supporting fish. Here we report the sequencing of complete 16,499 base pair (bp) mitochondrion genomes from four C. salinus salinus individuals. The mitochondrial genome of C. salinus salinus comprises 13 protein-coding regions, 12S and 16S rRNAs, 22 tRNAs, and an 832 bp D-loop region. The first reported single nucleotide polymorphisms (SNPs) were identified within the mtDNA of C. salinus salinus, with the four mitogenomes exhibiting only 0.0485% nucleotide sequence divergence indicative of low intraspecific variation. These complete mitogenomes will facilitate future genetic analyses of intraspecific diversity between the two described subspecies of C. salinus as well as other Cyprinodon pupfishes in southwestern North America.