The accumulation of allantoin and trace metals (TMs) in nine moss species was examined after the exposure to stress conditions. Both the environmental anthropopressure effect and laboratory-simulated stress conditions were monitored. Moss samples were collected from different locations, i.e. a non-TM contaminated area, an urban area, and a metalliferous area. The effect of Cd, Pb, Hg, Ni, Zn, salinity, and an acidic environment on the allantoin content was tested. Principal component analysis was performed to reveal the relationship between samples of different origin. Large differences in the metal and allantoin accumulation capability of mosses were noted between samples harvested from the different locations. Seven species were considered as potential metal accumulators, as they exhibited tolerance to elevated levels of heavy metals. The observed TM effect on the allantoin accumulation indicated TM pollution as an important environmental factor that can significantly influence the content of this compound in mosses. Further studies on the contribution of various environmental factors and individual characteristics of plant species are highly expected to recognize the trend in the accumulation of specialized metabolites and TMs in response to hazardous growth conditions.