| Summary: | In this study, the complete mitochondrial genomes of the Mexican golden trout, <i>Oncorhynchus chrysogaster</i>, and Nelson’s trout, <i>O. mykiss nelsoni</i>, were assembled and characterized. The mitogenomes were 16,655 bp and 16,661 bp long, respectively, and were composed of 13 protein-coding genes (PCGs), two ribosomal RNA genes, and 22 transfer RNA genes (all with typical ‘cloverleaf’ secondary structures). The length of the D-loop regions was among the longest found in Salmonids, and mitochondrial synteny in both species was identical to that reported in other Salmonids. Selective pressure analysis in the PCGs indicated that purifying selection, mainly among <i>cox</i> and <i>nd</i> genes families, likely generated the main differences between the two studied species. Nine tRNA genes showed slight differences relative to other <i>O. mykiss</i> subspecies, which were identical between the two study taxa. The origin of the light-strand replication has a loop that was especially large in <i>O. mykiss nelsoni</i>. Phylogenetic analysis indicated that <i>O. chrysogaster</i> and <i>O. mykiss nelsoni</i> are sister species, contrary to the expectation that <i>O. chrysogaster</i> would cluster with <i>O. gilae</i>. As previous studies have suggested, <i>O. chrysogaster</i> and <i>O. mykiss nelsoni</i> share common ancestry with North American trout species.
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