Flying fish has specialized pectoral fins. When they are activated, they will rush out of the water, expand their pectoral fins and flap their caudal fin to glide. The pectoral fins are controlled by two groups of muscles in which the external appearance is pink. No histological investigations have been made on their muscles to verify whether they are red muscles. The purposes of this study were to compare the pectoral fin muscle, trunk white muscle and trunk red muscle by histological and proteome methods so as to understand if the pectoral fin muscles is red muscles and to infer their function. Cyselurus poecilopteins was used for this study, Result show that the sizes for the cross section of the pectoral-fin-muscle-fibers were between the white and red muscles, and a large amount of connective tissue and fat tissues are present in the space among the muscle cells. It is interpreted the pectoral fin muscles of flying fish might not belong to white muscle and red muscle, and they probably utilize lipid metabolism to provide enough energy for the gliding activates. The proteomic pages for the three muscle types were compared and differences were found in the muscle proteins: actin, myosin regulatory light chain, myosin light polypeptide; enzymes: isocitrate dehydrogenase, malate synthase, queuosine biosynthesis protein¡Fstress proteins: heat shock protein (HSP70 and HSP60). Expressions of these proteins were high in the pectoral-fin muscles than in the white and red muscles. These results suggest that the flying fish¡¦ pectoral-fin muscles may involve in the oxidative and glycolysis pathways, and the muscle fibers type maybe belong to an intermediate type of muscle fiber.