Planctomycetes have been isolated from various hydric environments. These fastidious bacteria are overlooked by routine 16S rRNA gene-based PCR detection in hospital laboratories, and their presence has not been documented in the health-care environment. Using a specific culture protocol, we recently isolated a new, non-filterable Planctomycetes species, Gemmata massiliana, from one hospital water network. The goal of the study was to monitor the presence of G. massiliana in two hospital water networks. We developed a G. massiliana-specific real-time PCR system and monitored the presence of the Planctomycetes for 12 months in two hospital water networks, in filtered water collected at the intensive care unit and in non-filtered water collected from dental chairs, tanks, and usage points. Four of 180 (2.2 %) filtered water samples tested positive versus 23 of 204 (11.3 %) non-filtered points (p < 0.05), including 18 of 128 (14.1 %) dental chairs, 3 of 51 (5.9 %) usage points, and two of 25 (8 %) tank specimens. There was no significant difference in the prevalence of G. massiliana between the two hospitals (p > 0.05). However, this organism was detected significantly more frequently during April and September than the 10 other months. Because G. massiliana is deeply entrenched in the hospitalized patient's environment, evaluating this organism as a new opportunistic, health-care-associated pathogen is warranted.