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In this article we report the complete mitochondrial genome of the Warm Springs pupfish, Cyprinodon nevadensis pectoralis. The genomic DNA of a single female individual was extracted and sequenced on the Illumina HiSeq2000 platform. It contains 16,499 bp and a total of 37 genes, divided into 22 tRNA genes, 2 rRNA genes and 13 protein-coding genes. It exhibits 94% sequence similarity with the other published mitochondrion in its genus, C. rubrofluviatilis. A Tamura-Nei maximum-likelihood tree constructed from mitochondrial sequences shows expected phylogenetic relationships between C. nevadensis and sister taxa.