Some Mallotus species are commonly used as traditional medicine (TM) ingredients in Vietnam and China, but only a few are studied for their activities. In Part I, high-performance liquid chromatography (HPLC) fingerprints of 39 Mallotus samples (17 species) were developed and, because of the complexity of and the large differences between the samples, it was chosen to analyse the unaligned fingerprints. The peaks, potentially responsible for the antioxidant activity in given Mallotus species, were indicated by the regression coefficients from an orthogonal projections to latent structures (O-PLS) model. In the present study, an in depth discussion on the need for alignment of the Mallotus fingerprints for the indication of the potentially active compounds is made, as well as an experimental analysis and identification of the previously indicated peaks by HPLC-mass spectrometry (HPLC-MS). Additionally, to thoroughly study and discuss the alignment problem, the modelling and prediction of the antioxidant activity of green tea samples based on HPLC fingerprints were also considered.