The family Ephippidae consists of eight genera and 15 species. The genus Platax with five species distributed throughout Indo-Pacific, seemingly has more diversity than other genera of the family. Phylogenetic relationships among species and genera of the family, however, are not fully resolved. 48 sequences of eight species (four genera) of batfishes are available in the GenBank and have been used to construct the molecular phylogenetic tree of Ephippidae for the present study. Based on the present analysis, a species of Chaetodipterus, C. faber is located at the farthest distance from other studied genera of this family. This positioning, confirm the previous morphological study based on osteology. Three other examined genera Ephippus, Platax and Tripterodon are grouped together under a supported clade. The genus Platax is probably a paraphyletic taxon regarding to the positions of the genera Tripterodon and Ephippus in the phylogenetic tree. Three species of Platax, P. orbicularis, P. teira and P. boersii are clustered together while two other species, P. batavianus and P. pinnatus are in another cluster. Molecular phylogeny of Platax species are somewhat consistent with the dental characteristics and fin ossification of the members of this genus.