Percomorpha is the most diverse group of Acanthomorpha, and the interrelationships among the members are unsettled. Perciformes, one order of Percomorpha, is the largest fish order with 160 families placed in 20 suborders. The relationships among the suborders of Perciformes remain conflicting between the hypotheses of phylogenetic relationships based on different characters. Presently, major studies on relationships of higher taxa are from Japanese based on the mitogenome, and the other studies were based on nuclear gene sequences. Mok recently suggest a hypothesis of the Gobioidei, it is the sister group to a clade which includes the Callionymoidei, Dactylopteriformes, and possibly Pegasidae, based on osteological characters. Following this, a phylogenetic hypothesis of the Callionymoidei based on mitochondrial and nuclear genes was conducted, and the Taiwanese and Australian specimens of G. buergeri might be treated as different species. Morphological differentiation in the sagitta in these two groups points to the same conclusion. The Pempheridae is the sister group of the Glaucosomatidae that is demonstrated by molecular evidences. It is the same with the relationship based on the morphological characters, such as otolith and swimbladder, etc. The monophyly of Callionymoidei is not recovered in this study. The Syngnathoidei may be the closest group of Callionymidae, and the Gobiesocoidei is suggested to be closest with Draconettidae. In the application of mitogenomic information, the sequcences selected by Japanese have not been decided to be unsaturated, so I made statistical inference of the variation for mitochondrial sequences and selected nuclear genes. I have found out the variation-saturated genes and discuss the application of these sequences to phylogenetic studies derived from these datasets in this study. Advisors/Committee Members: Shao, Kwang-Tsao (chair), Mok, Hin-Kiu (committee member), Cho, Chung-Lung (chair), Chang, Hsueh-Wen (chair), Tzeng, Chyng-Shyan (chair).