A phylogeny was generated for Leiognathidae, commonly known as ponyfishes, using nucleotide characters from two mitochondrial genes. Results indicate that Leiognathidae comprises two major clades, one consisting of species that exhibit internally sexually dimorphic light-organ systems (LOS), and the Leiognathus equulus species complex, whose members exhibit neither internal nor external sexual dimorphism of the LOS. Species with internally sexually dimorphic LOS generally also exhibit associated male-specific external modifications in the form of transparent patches on the margin of the opercle, the midlateral flank, or behind the pectoral fin axil. The L. equulus species complex is the sister group to all other leiognathids, and a new species, L. robustus, recovered within this clade is described herein. Results demonstrate that Leiognathus is paraphyletic, whereas Gazza and Secutor are each monophyletic and are nested within the sexually dimorphic clade. The morphology of the LOS of non-sexually dimorphic leiognathids is compared to the more common sexually dimorphic state, and differences in these systems are discussed and illustrated. In the context of a family-level phylogeny, we can trace the evolution of the leiognathid LOS from a “simple” non-sexually dimorphic circumesophageal light organ to a complex and species-specific luminescence system involving not only major structural modifications of the light organ itself but also numerous associated tissues.