Thirty-two different basidiomycete isolates were inoculated separately into contaminated soil and the soil colonization ability was assessed visually. Large differences in the colonization ability and growth patterns were found between the different fungi. Phospholipid fatty acids (PLFAs) were extracted from the soils of the seven isolates with the best colonizing ability. All PLFAs that were not found in pure cultures of the seven fungi were considered as bacterial PLFAs. The bacterial PLFA data were subjected to principal component analysis (PCA) to indicate changes in the indigenous bacterial community. The experiment was repeated in a sandy agricultural soil. The bacterial PLFA patterns were altered when fungi were inoculated into soil, irrespective of whether it was polluted or not. In particular the PLFA cy19:0, indicative of Gram-negative bacteria, was higher in fungal-inoculated soil than in uninoculated controls. The PLFA patterns for each fungal treatment were distributed more or less similarly in the PCA plots of both contaminated and sandy agricultural soil. Soil inoculated with Antrodia vaillantii, Hypholoma fasciculare or Recinicium bicolor was considerably different from the control along PC 1. Soil inoculated with Phanerochaete chrysosporium was characterized by different values along PC 2 compared with the other fungal soils.