The family Leiognathidae, commonly known as ponyfish or slip mouth, comprises three genera, each being characterized mainly by mouth morphology. To date, however, neither the phylogenetic relationships within the family nor monophyly of the genera has been tested. The phylogenetic relationships among 14 species of Leiognathidae, inferred from two protein coding mitochondrial genes (ND4 and 5), indicated monophyly of the studied species form genera Gazza and Secutor, and paraphyly of the genus Leiognathus, with L. equulus occupying a basal branch of the family. The relationships allowed phylogenetic analyses of mouthpart structures and light organ systems. The results suggested that the morphology of the upwardly and forwardly protractile mouth types (latter with canine-like teeth) are phylogenetically informative, and the downwardly protractile mouth type being ancestral in the family. The results also suggested that internal sexual dimorphism of the light organ system was present in the common ancestor of a sister clade to L. equulus, whereas external sexual dimorphism seems to have evolved subsequently in two monophyletic subgroups.