A study of the distribution of fungal microflora was conducted on the sediment of Lake Alimini Grande in order to contribute to the evaluation of the ecosystem characteristics that can effect the process of decomposition. The isolation and identification of fungal species and ergosterol analysis were performed on sediment samples taken from 33 monitoring stations in autumn and winter. Altogether, 24 strains belonging to 8 genera were isolated. Trichoderma spp (41.6%) and Aspergillus spp (20.8%) were the dominant genera: in particular, Trichoderma was present near the Traugnano marsh, whereas Aspergillus was isolated in the area of connection to the sea