A series of epipolythiodioxopiperazines in the fungus Chaetomium cochliodes was investigated using reversed-phase liquid chromatography with diode array detection and electrospray quadrupole time-of-flight-type tandem mass spectrometry in the positive ion mode. The fragmentation of protonated molecular ions including low-abundance parent ions, [M+H]+ for five known epipolythiodioxopiperazines, dethiotetra(methylthio)chetomin, chaetocochins A-C, and chetomin, was carried out using low-energy collision-induced electrospray ionization tandem spectrometry. It was found that McLafferty rearrangements occurred in the CID processes and produced a complementary pair of characteristic fragment ions containing piperazine rings (fused and unfused), especially to determine the number of S atoms on each ring. The fragmentation differential between [M+H]+ and [M+Na]+ was uncovered. Complementary fragmentation information obtained from [M+H]+ and [M+Na]+ precursor ions is especially valuable for rapid identification of epipolythiodioxopiperazines. A likely known compound, possibly related to chetoseminudin A, and three new species of epipolythiodioxopiperazines from the fungus C. cochliodes were identified or tentatively characterized based on tandem mass spectra of known ones.