In the present work, a novel strategy including the use of two different comprehensive HPLC methods has been employed to study the whole carotenoid composition of mandarin essential oil. Thus, two different fully orthogonal two-dimensional HPLC methods have been used. A silica microbore column was coupled to a C(18) monolithic column to study the mandarin saponified extract, while the coupling of a cyano microbore column to a C(18) monolithic column was employed to study the intact mandarin essential oil sample in order to characterize the native carotenoid esters composition. Detection was performed by connecting a photodiode array detection (DAD) system in parallel with a MS detection system operated with an atmospheric pressure chemical ionization (APCI) interface. Thus, the carotenoid identification was carried out by combining the information provided by the DAD and MS systems and the peaks relative position in the two-dimensional chromatograms.