Legionella spp. is considered an emerging microorganism involved in aquatic environments contamination and cause of Legionnaires' disease. The aims of the study are to evaluate the level of contamination of Legionella spp. in the water system of the largest Hospital of Apulia region during a 4-year surveillance and to establish, by molecular method, the presence of a predominant genotype of L. pn. sg 1. The results showed that Legionella spp. was present in 36% of water samples with Legionella pneumophila serogroup 1 (L. pn. sg 1) the most prevalent species and serogroup and the wards most contaminated are the high risk units. In addition, despite four main clones of L. pn. sg 1 were identified, a predominant genotype existed. In conclusion the study demonstrates the necessity for periodic evaluation on hospitals water system to assess the potential contamination of Legionella spp., performing decontamination in the presence of bacterial contamination, even low, in particular in high risk wards. Moreover, the switching of the disinfection methods may be suggested in order to prevent resistance phenomenon by some L. pn. sg 1 clones.