Isolates of Aspergillus niger, selected from coal dust sediment of a mine containing As (400 mg/kg), pH 3.3-2.8, and from river sediment found near the mine (As, 363 mg/kg, Sb, 93 mg/kg), pH 5.2-4.8, growing on Czapek-Dox agar exhibited distinct responses in the mycelial growth in arsenic contaminated environments. The radial growth of the isolate from the coal dust in comparison to the control strain from an environment without pollution was reduced approximately to one-half. It formed black, very small compact colonies, with dense sporulation. The opposite, the strain from the river sediment, grew better in Czapek-Dox agar like the control. It formed larger colonies with dense centre and strong sporulation. Also, the culture from river sediment developed faster than the coal dust isolate and control strain. Differences were also recorded in size and thickness of conidia heads, phialide, metulae, and conidiophores. Both isolates from contaminated localities exhibited higher tolerance to exogenic toxic effects of As5+, Cd2+ and Cu2+ (5, 25 or 50 mg/l) than the control culture. Tolerance was monitored using the growth of biomass in liquid Czapek-Dox medium. We confirmed the morphological identification of our isolates to A. niger species with the PCR method. The results refer to complicated relations between biotic and abiotic effects that may directly affect the processes observed in the in situ environment.