Long-range transported atmospheric pollutants (or transboundary pollutants) include trace metals with isotope ratios and compositions that vary from those of domestic pollutants, which threaten mountain ecosystems. These differences can be applied as indices (trace metal indices) to evaluate the influence of transboundary pollutants on mountain ecosystems. Mosses play important ecological functions in mountains and are sensitive to atmospheric deposition. Therefore, using these indices for moss biomonitoring can provide a more accurate indication of ecosystem health. However, few studies have examined which indices are appropriate for moss biomonitoring. In this study, the effectiveness of moss biomonitoring using trace metal indices was examined for evaluating transboundary pollutants in mountainous areas in Japan. Transboundary pollutants in these areas originate from mainland Asia and are characterized by high lead isotope ratios, lead to zinc (Pb/Zn) ratios, and arsenic to vanadium (As/V) ratios. Given that the abundance of transboundary pollutants decreases with distance from mainland Asia, moss isotope indices are also expected to vary with distance. Based on observations, Pb isotope ratios were found to decrease with distance from mainland Asia; in contrast, Pb/Zn and As/V ratios did not display any notable relationship with distance. These results are likely attributed to biological and environmental factors that affect trace metal contents in moss. Thus, moss Pb isotope ratios are useful indicators of transboundary pollutants in Japan’s mountains, offering an important tool for comparable moss biomonitoring studies in East Asia.