The sea urchin genus Tripneustes has historically served as a model species for theories on population divergence due to its impressive pan-tropical distribution with few well documented barriers to dispersal. While showing very little localized variation, analysis of microsatellite markers and mitochondrial COI sequences suggests that greater isolation exists within the Pacific Ocean than previously believed. A draft transcriptome has allowed for the generation of a full mitochondrial genome sequence from the central Pacific T. gratilla, and is compared to mitochondrial genome assemblies across major sea urchin families. The genus Tripneustes is placed in a broader phylogenetic context and tree node calibrations are used to date the origin of the lineage. Rates of codon variation in the 13 coding sequences of the mitochondrial genomes across the families are assessed, and pairwise dN/dS (ω) ratios highlight variable contraints on coding regions among the sea urchins. Increased understanding of the genomics of such a broadly distributed animal, with an available reference genome in Strongylocentrotus purpuratus, and an effectice Wright-Fisher approximating population, could allow for Tripneustes to be an effective model organism for population genomics.