Family Pinguipedidae belong to the class Actinopterygii, subclass Neopterygii, order Perciformes, suborder Trachinoidei. Currently the interrelationships of the genera within this family and among the families in the Trachinoidei remain unequivocal. Also, whether the Cheimarrichthys should be included in the family Pinguipedidae has also been a controversial issue. This study aimed to reconstruct phylogenetic hypotheses in order to resolve these questions. Species of the Parapercis and Kochichtys in the family Pinguipedidae occur Taiwan. This study used osteological characters, 16S rRNA and Cyt b sequences to conduct phylogenetic analysis such that hypotheses can be proposed. The results revealed the monophyly of Parapercis, a taxonomic view consistent to the prevailary classification. Summarizing all the results, the 17 Parapercis species analysed can be divided into 4 groups. They are (1) Parapercis aurantiaca¡BP. decemfasciata¡BP. mimaseana¡BP. multifasciata¡BP. muronis¡Btwo morphotypes of P. sexfasciata¡F(2) P. cephalopunctata¡BP. clathrata¡BP. hexophthalma¡BP. kamoharai¡BP. tetracantha¡BP. xanthozona¡F(3) P. cylindrica and P. snyderi¡F(4) P. maculata¡BP. ommatura and P. somaliensis. Two color morphotypes have been shown for Parapercis sexfasciata. Data of the present study revealed that the ¡§ autapomorphic¡¨ osteological character known only in Kochichtys also occurred in three Parapercis species. This result supports a close relationship between these species. However, it also challenges the validity of the generic status of Kochichtys. About the dabate of the phylogenetic position of Cheimarrichthys, it should be put into its own family, Cheimarichthyide, rather than placed in the Pinguipedidae. The hypothesis for the sister group of Pinguipedidae to the Cheimarichthyide is not supported by all the data in this study completely. Morphological and molecular evidences are incongruence for closest phylogenetic relationship. Similar results were also obtained when the molecular sequences were analysed using different methods. More data analyses are needed for complete and reliable results. The present study suggests that the Trachinoidei is not a monophyletic group.