This research was carried out with the aim to explore the heterotrophic microbial population of two sediments in different oxic conditions of the Lake of Lugano (Lago di Lugano). The values of the viable bacterial counts found in our sediment samples were typical for an eutrophic lake. The increase in the proportion of anaerobic to aerobic bacteria at 30 °C observed in the sediment samples of Agno may reflect the depletion of oxygen concentrations in the water column. The genera Aeromonas, Pseudomonas, Bacillus and Clostridium, as well as strains belonging to the Coryneform-group, represented the major taxonomic groups of heterotrophic bacterial communities in the water-sediment interface.