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The Mohave tui chub (Siphateles bicolor mohavensis) is an endangered cyprinid fish endemic to the Mojave Desert region of southeastern California, USA. Here, we describe the complete 16,607 base pair (bp) mitochondrial genome of S. b. mohavensis. The mitogenome has a nucleotide base composition of A (29.08%), T (26.91%), G (17.58%), and C (26.43%), and encodes 13 protein subunits, 22 tRNAs, a 12S rRNA of 956 bp and 16S rRNA of 1691 bp, and a 929 bp D-loop control region, each located in the conserved mtDNA structure typical for cyprinid fishes. All protein-coding genes have initiation codons of ATG or GTG, and only the ND1, CO1, ATPase8, NDL4, ND4, ND5, and ND6 genes have complete stop codons. Phylogenetic analyses confirmed the relationship of S. b. mohavensis to several genera of cyprinids (e.g. Gila, Acrocheilus) also endemic to western North America. This characterized mitogenome may help inform management practices for S. b. mohavensis by facilitating future studies on how allopatric populations of this imperiled species are evolving across refuge habitats.