Our objective, as part of the planned conservation work, was to identify culturable fungi related to the formation of various deterioration symptoms occurring on the Spectatius family marble tomb, the largest monument of the Roman Necropolis in Šempeter, Slovenia. By using fluorescent microscopy, microbial cultivation methods and standard DNA sequencing we were able to identify 21 fungal isolates, 16 being filamentous moulds, primarily dominated by xerophilic Cladosporium spp. (mainly Cladosporium langeronii RN 28) and some Alternaria species; and 5 yeast or yeast like species namely Torula fici, Filobasidium wieringae, Rhodotorula babjevae and Blastobotrys peoriensis. Locations on the tomb, which are well sheltered against rainfall, contained higher concentrations of xerophilic fungi to those, which are completely or partially exposed to rain. The black fungal species of Cladosporium spp. and Alternaria spp. formed the bulk of melanized-greyish patina present on the bottom reliefs and within the cracks of the inner dome of the Spectacius tomb. Moreover, the red coloured yeast R. babjevae caused a thick red pigmentation right under the top roof of the monument’s left side. The obtained results indicated that not only moulds but also yeasts can cause significant biodeterioration. Lastly we isolated indigenous mycoparasitic strains of F. wieringae (RN 37 and RN 38) that could potentially be used in biocontrol formulations applicable in situ for the sustainable preservation of the Spectatius family tomb monument.