A methodology of substantiating the ecological risk of technogenic soil pollution has been described according to the results of bioindication using microfungal communities. At the first state, the values of the factors under which the frequency of each species is maximal were estimated using ordination methods. The statistical distribution of the species sensitivity was simulated according to these data. The methodology was illustrated using the results of analysis of the toxicity of soil samples from uranium mine dumps (the village of Kadzhi-Sai, Kyrgyzstan). The preliminary estimates of the critical values of six soil pollution indices that provide the defined allowable probability of the ecological risk have been given.