In Greece, standard tests are performed in watering and cooling systems of hotels. A total of 1,494 water samples were collected during 2004-2011 from 124 hotels from four regions in Crete (Greece). Samples were tested for the presence of Legionella spp.; 103 isolates were identified and typed by polymerase chain reaction (PCR)-sequencing and sequence-based typing (SBT) (in case of L. pneumophila sg 1). Of those, 48 belonged to various serogroups of L. pneumophila (sg 1, 2, 3, 5, 6, 8, 12, 13, and 15), 32 were characterized as L. anisa, 17 as L. taurinensis and there was a single occurrence of L. quinlivanii, L. maceachernii, and L. oakridgensis. In the case of L. pneumophila SG1, one prevalent sequence type was revealed (ST37). The variability of Legionella spp. observed questions the existence of a single ST of the L. pneumophila sg1 species and leads towards the need for a genetic level investigation of all Legionnaires' disease cases.