The Galapagos sea lion, Zalophus wollebaeki, is a pinniped endemic to the Galapagos archipelago. The objectives of the study were to extract DNA from a fresh scat sample, and to sequence and assemble the mitogenome. We think the significance lies in the unusual method of DNA recovery, considering that Z. wollebaeki is an endangered species and sampling could be a difficult task. In addition, we hope that this methodology can be used in other research with marine mammals.