• The effects of environmental heavy metal pollution on the genetic structure of pioneer populations of the ectomycorrhizal basidiomycete Suillus luteus were assessed.• Sporocarps were collected from nine different locations and characterized by amplified fragment length polymorphism (AFLP) markers. Six of the sampling sites were contaminated with heavy metals and were dominated by tolerant individuals.Considerable genetic diversity was found within geographic subpopulations, but no reduction of the genetic diversity of populations inhabiting contaminated soils was observed. Neither did significant clustering of subpopulations inhabiting contaminated soils occur. Overall, the genetic differentiation between subpopulations was low, but Bayesian inference indicated the presence of two genetically differentiated clusters of individuals, which may correspond to different intercompatibility groups in S. luteus.• Heavy metal contamination seems to have a limited influence on the genetic structure of populations of S. luteus. Loss of diversity may have been prevented by sexual reproduction and rapid evolution of the tolerance trait or initial genetic bottlenecks may have been reduced by admixture and recurrent migration from surrounding populations colonizing noncontaminated soils.