The complete mitochondrial genomes of two imperiled species endemic to the Southwestern United States: Peppered Chub () and Gila Trout ().

and are fish species endemic to the Southwestern United States. We present the complete mitochondrial genomes for these species. Each genome consisted of 13 protein-coding genes, two ribosomal (rRNA) genes, 22 transfer RNA (tRNA) genes, and the control region (D-loop). Mitogenome lengths were 16,916 base pairs (bp) for , and 16,976 bp for The GC content was 41% for and 46% for . The relationships of and were consistent with previous phylogenetic analyses.