In the previous paper from this series, we proposed mass spectrometric fingerprinting of complex botanical samples upon the examples of the pharmacologically important phenolic acids and flavonoids selectively extracted from Salvia lavandulifolia. In this study, we explore fingerprinting efficiency with a novel two-dimensional analytical system composed of the reversed-phase thin-layer chromatography and the reversed-phase high performance liquid chromatography with mass spectrometric detection (2D RP-TLC-RP-LC-MS). We also compare its efficiency with that of the one-dimensional analytical system (the reversed-phase thin-layer chromatography with mass spectrometric detection; 1D RP-TLC-MS). As our present study is basically focused on the method development, we considered it as justified to carry out our comparison with the phenolic acid extracts selectively derived from the Salvia lavandulifolia species, similar as it was done in Part II from this series. Upon the results obtained, it was established that the 1D RP-TLC-MS mode and the 2D RP-TLC-RP-LC-MS mode can be applied to fingerprinting of herbal extracts, and that the 2D RP-TLC-RP-LC mode can provide a more abundant information than that originating from the 1D RP-TLC mode.