Abstract Biological indicators are widely used to monitor genotic compounds and air quality in urban environments. Parmotrema tinctorum and Teloschistes exilis have been used to verify the presence of pollutants and analyze morphophysiological alterations in the thallus of species caused by their action. Species were exposed for seven months, in an urban area, in southern Brazil. Mutagenicity and cytotoxicity of PM10 organic extracts were assessed in the Salmonella/microsome assay at two stations. High concentrations of S, Pb, Cr, Zn and Hg were registered in the last period of exposure and more significant morphophysiological damages were verified in the lichens. Generally a higher mutagenic activity is observed in organic extracts of airborne particulate matter during the first months and in the third period of exposure of lichens. In addition, nitro compounds was detected through nitro-sensitive strains. Lichens and mutagenic biomarkers enabled the evaluation of air quality and the presence of environmentally-aggressive compounds.