Black Aspergilli are widespread molds inhabiting different substrates. In addition to their many positive roles in biotechnology and food industry, they can also be harmful because of their allergic, invasive and toxic potential. This paper aimed to compare the cytotoxicity of mycelium extracts of different isolates of A. piperis and A. luchuensis species because of their morphological and phylogenetic relatedness and because of their incidence in the air and dust in indoor environments in which they can be harmful to the respiratory system of exposed people. In this paper was tested the cytotoxicity of mycelium extracts of nine isolates of A. piperis and A. luchuensis species on A549 human lung adenocarcinoma cells. The assay was performed by treating A549 cells with different concentrations (0.025 - 0.8 mg/ml) of mycelium extracts of each isolate for 24 hours. The viability of treated cells was measured by MTT cytotoxicity assay relative to the controls, and the concentrations inhibiting the growth of 50% cells - IC50 were calculated. All tested mycelium extracts proved to be cytotoxic on A549 cells. The most toxic was the mycelium extract of A. piperis isolate MFBF AN12614 which decreased viability of A549 cells by 90% at a concentration of 0.025 mg/ml. The least toxic was mycelium extract of A. piperis MFBF AN12404 with IC50 of 0.5068 mg/ml. Mycelium extracts of A. luchuensis species showed pronounced toxic potential and IC50 of all four tested mycelium extract were lower than 0.1 mg/ml. Considering IC50 of 0.03 mg/ml, extract of airborne isolate MFBF AN10927A from a grain mill was the most toxic among the examined mycelium extracts of A. luchuensis species. The results of this study indicate the complexity of metabolite composition in extracts of individual isolates of A. piperis and A. luchuensis species and the toxic potential is characteristic of an individual isolate regardless of species. Thereby, the results are consistent with a high degree of phylogenetic relatedness. Because all tested isolates of A. piperis and A. luchuensis proved to be cytotoxic on A549 cells, inhalation of airborne or dustborne toxinogenic mycoparticles may cause damage in respiratory system of exposed people, regardless of the type of indoor environment or water damage.