Gas phase decomposition of metal cation complexes of methyl naphthoate isomers were studied by using collision induced dissociation tandem mass spectrometry with electrospray as a method for generation of ions in the gas phase (ESI-CID-MS/MS). From among the metal cations used, lithium, calcium and zinc complexes were found to be useful for differentiation of methyl naphthoate isomers. For lithium and calcium complexes, the differentiation can be made on the basis of relative abundances of fragment ions. For zinc complexes there was a significant qualitative difference between the CID MS/MS spectrum of methyl 1-naphthoate and the CID MS/MS spectrum of methyl 2-naphthoate.