Some fishes use sound to communicate. The majority of these soniferous fishes use superfast sonic muscles to set the vibration of the swim bladder which results in sound emission and sound amplification. Carapus, a benthic ophiidiform genus, use a slow contracting sonic muscle to pull the anteriormost part of the swim bladder, upon termination of the pulling action, the front part of the swim bladder is snap back setting the swimbladder fenestrum to vibrate. This vibration gives rise to the sound. Other ophiidiform fishes may also use a similar way to emit sounds. Among the soniferous percoids, an advanced perform suborder, glaucosomatid, pempherid, and terapontid share a fenestrum-like structure in the front part of their swim bladder. Previous molecular study suggested that the first two groups form a clade (monophyletic group). It is of great interest to compare the proteomic features of these groups with that of the ophiidiform representatives so that the effects of function and phylogeny to the proteomic characteristics of the sonic muscle can be compared. A species was selected for each of these four groups and their proteomics were analyzed. Results of this study, however, revealed the protein composition of the sonic muscles in the ophiidiform species was more similar to that of the pempherid species. The proteins contribute to the close relationship between these two groups was discussed. A total of 484 protein spots were found in these four species and only five were presented in the sonic muscles of all four species, but absent in the white muscles; and only three of them were successfully identified as: Flotillin-1 (spot 6), HBS1-like protein (spot 8), and Ras-related protein ralB-B (spot 10). Their functions which may be related to the specific role of the sonic muscle were discussed.