The mitochondrial genome of the long-spined black sea urchin, Diadema antillarum, was sequenced using next generation sequencing technology. The long-spined black sea urchin, Diadema antillarum is a freely living marine benthic invertebrate that inhabits the shallow waters of the Western Atlantic Ocean and Caribbean Sea. It is an important herbivore and keystone species that helps maintain healthy coral reef systems along its coastal marine habitats. Very few mitochondrial sequences have been reported to date. The results from this study has provided some insight into the dispersal and speciation events of the family Diadematidae.