In a continued effort to understand the rapid evolution of insular dwarfism and gigantism, we have sequenced the complete mitochondrial genomes of 14 specimens of Crotalus mitchellii, the Speckled Rattlesnake, from across its range. The Crotalus species complex is distributed throughout the SW US and NW Mexico, including a number of islands in the Sea of Cortez where mean body size ranges ten-fold between populations on the smallest and largest islands. Although there may be ecological explanations for some part of this dramatic phenotypic divergence, initial sequencing efforts of three loci revealed unexpected phylogenetic relationships among populations of giants and dwarves. To further explore the puzzling phylogeographical pattern within the complex, as well as to identify the genetic underpinnings of a rarely observed case of rapid body size evolution in vertebrates, we sequenced the whole genome and analyzed the locus-specific substitution rates and phylogenetic relationships among mitochondrial genes. Given the critical role of mitochondria in metabolism and growth, this genome is of particular interest in this study system. Substitution rates vary substantially among genes and individuals and there is a signature of hybrid introgression between distant mainland populations. Both the power and risk of using mitogenomic datasets for understanding short- and long-term dynamics in this species complex, as well as others, will be discussed.