Twenty five fungal isolates were collected from mural paintings, air and stone surfaces at Tell Basta tombs and were attributed to Aspergillus versicolor, A. japonicus, A. restrictus, A. terrus, A. fumigatus and A. nidulans, Fusarium oxysporum and Penicillium sp. Moreover, A. japonicus was the most present in the total fungal samples. The isolated fungi showed to be involved in fading of azurite blue and red hematite pigments due to the bioaccumulation of copper (Cu) and iron (Fe) ions, respectively, on the fungal cell wall. Fe ions enhanced the biomass, but Cu ions enhanced melanin production. Thymol was used with different concentrations (10, 20, 30, 50, 100 µg/ml) to inhibit the fungal growth and the concentration 100 µg/ml was the most effective. Isolated fungi varied in their resistance profile to the tested thymol concentrations since Penicillium sp. was the most resistant, but A. japonicus was the most sensitive. Thymol caused yellowing of the treated surfaces, so fumigation method was recommended. Furthermore, fumigation reduced the microbial colonization of paintings significantly. On the other hand, thymol caused color change neither for the tested pigments nor for the appearance of stone surfaces.