The complete mitogenome of Echinometra sp. EZ has been described and fully annotated in this study. Phylogenetic analysis of cytochrome c oxidase subunit I (COI) from six Echinometra species confirms that our sample is E. sp. EZ. The mitogenome is 15,698bp in length and contains 13 protein-coding genes, 22 tRNAs, 2 rRNAs, and a non-coding region with an identical organization to other Echinoidea. The E. sp. EZ mitogenome shared $99.1% identity to the published Echinometra mathaei mitogenome, differing by 147 SNPs. The E. sp. EZ mitogenome will serve as a resource that can be applied to disen- tangling the Echinometra species complex and to future population genetic studies of this ecologically important sea urchin species.