Species turnover within a genus is often observed across climatic gradients. Mitochondrial (mt) divergence between species is usually thought to be a neutral process, but mt haplotypes within and among species often segregate with climatic factors known to impact mitochondrial function. For this reason, climatically-driven evolution of the mt genome might be an important driver of ecological speciation, and, through epistatic interactions with the nuclear genome, a driver of post-zygotic isolation. Although studies frequently report the signature of positive selection on particular mt genes in high-elevation species and posit adaptive explanations, there is little evidence to say whether elevation consistently causes selection across mt genes and in all taxa. To investigate how elevation shapes mt divergence, we analyzed the signature of natural selection on the protein-coding regions of the mt genome. We obtained mitogenomes from 186 terrestrial vertebrates consisting of sister taxa from high and low elevations at similar latitudes as well as low-elevation outgroups. Ratios of nonsynonymous to synonymous substitutions (dN/dS), a measure of positive selection, generally increased in high-elevation species. However, this difference was only significant in cases where a model of evolution estimating the same dN/dS value for the low-elevation and outgroup taxa was preferred to one with more parameters. This suggests that there is positive selection on the mitochondrial genes of high-elevation vertebrates, particularly where they have evolved from within consistently lower-elevation clades. We discuss implications of these findings for environmental adaptation, speciation, and climate change, as well as refinements in methodology and an exploration of mitochondrial responses to elevation in invertebrates.