This study presents a comparison of trace (Hg) and criteria (CO, SO2, NOx, O3 and PM10) air pollutants monitored at two remote sites with the same latitude but different altitude: Mt. Lulin and the Penghu Islands, in Taiwan from 2011 to 2012. A filtering technique was comprehensively applied to distinguish the climatic characteristics of the two remote sites, as well as to determine their discriminant factor. The concentrations of air pollutants monitored at Mt. Lulin were generally lower than those at the Penghu Islands, with the exception of O3 concentration. PM10 and NOx were the important factors that can distinguish two clusters of measurement data at the two remote sites, and a criteria discriminant factor of atmospheric parameters derived from these two air pollutants. For both high- and low-frequency patterns, the concentrations of NOx and PM10 exhibit significant differences between the two remote sites. However, O3 concentrations showed almost no differences between these two remote sites, implying that the pattern for the formation and transportation of O3 at these two sites resulted from similar mechanisms. Moreover, atmospheric mercury (TGM) had a very good linear correlation with CO. The diurnal variation of Hg concentration was dramatic at the Penghu Islands, while it appeared as low as the North Hemisphere background mercury concentration at Mt. Lulin, indicating that they were not formed via the mechanism modes. This study thus proposed “scenario mercury” and “background mercury” for interpreting this interesting phenomenon.