Nitrogen (N₂) fixation by moss-associated cyanobacteria is an important N source in pristine ecosystems. Previous studies have shown that moss-associated N₂ fixation is sensitive to anthropogenic N pollution. However, we still lack understanding of the effects of other factors derived from anthropogenic sources, such as heavy metal pollution on N₂ fixation. To test this, we collected two dominant mosses (Pleurozium schreberi and Spaghnum palustre) from a temperate bog in Denmark and assessed their N₂ fixation responses to simulated heavy metal pollution by adding 5 levels (plus a control) of copper (Cu, 0–0.05 mg g dw⁻¹) and zinc (Zn, 0–0.1 mg g dw⁻¹). Metal concentrations in both mosses increased linearly with Cu and Zn addition, but N₂ fixation activity associated with S. palustre was to a greater extent negatively affected by both Cu and Zn additions than that associated with P. schreberi. Copper additions even promoted N₂ fixation in P. schreberi. Hence, the heavy metal sensitivity of N₂-fixing cyanobacteria is dependent on the host moss-species, and the vulnerability of ecosystems towards heavy metal pollution could vary depending on the dominant moss species.