The goatfish genus Mulloidichthys is abundant on reefs throughout the tropics. Characteristic of this genus is a long larval and pelagic juvenile phase, which could potentially confer large dispersal capacity. We sampled its mitochondrial DNA to answer the following questions: What speciation events have led to the formation of the extant species? How do they correlate with geological and oceanographic events? Are M. dentatus and M. martinicus geminate species formed by the rise of the Isthmus of Panama? Is there genetic structure between conspecific populations?