Coconut oil (CO) from fifteen different varieties of coconuts (Cocos nucifera L.) and one CO processed on an industrial scale were analyzed by electrospray ionization mass spectrometry (ESI-MS) and the data processed using the chemometric tools principal component analysis and independent component analysis. ESI-MS fingerprinting of lipid compounds showed predominance of diacylglycerols and triacylglycerols, as confirmed by high-resolution MS measurements. Chemometric processing of the ESI-MS data differentiated the coconut oil samples, showing that different coconut varieties/cultivars produce oils with distinguishable abundances of lipidic compounds. Thus ESI-MS analysis followed by data treatment using chemometric tools offers a tool able to classify the industrial coconut oils in a fast, simple and effective way, as well as serving as a potential method to identify the coconut varieties by the CO origin, and the occurrence of any adulteration. The procedure may also be applied for quality control of the industrial processes.