After the Elizabethkingia anophelis outbreak in Wisconsin, USA, an active search for the detection of the microorganism in hospital water systems from Central and Northern Greece was performed from June to December 2016. In total, 457 water samples from 11 hospitals were analyzed. Elizabethkingia spp. was detected in three samples collected from two hospitals, both of which are located in Northern Greece. Two of the three isolated strains were identified as Elizabethkingia anophelis. No cases of Elizabethkingia infection were reported in either hospital during 2016. This is the first reported isolation of the pathogen in water supply systems in Greece.