Two novel bacteria of the phylum Proteobacteria were isolated during searches for amoebaresistant micro-organisms in natural and constructed water systems. Strain HT99 was isolated from amoebae found in the biofilm of an outdoor hot tub in Cookeville, Tennessee, USA, and strain CC99 was isolated from amoebae in the biofilm of a cooling tower in the same city. Both bacteria were Gram-stain-negative cocci to coccobacilli, unculturable on conventional laboratory media, and were found to be intranuclear when maintained in Acanthamoeba polyphaga. The genomes of both isolates were completely sequenced. The genome of CC99 was found to be 3.0 Mbp with a 37.9 mol% DNA G+C content, while the genome of HT99 was 3.6 Mbp with a 39.5 mol% DNA G+C content. The 16S rRNA gene sequences of the two isolates were 94 % similar to each other. Phylogenetic comparisons of the 16S rRNA, mip and rpoB genes, the DNA G+C content and the fatty acid composition demonstrated that both bacteria are members of the order Legionellales, and are most closely related to Coxiella burnetii. The phenotypic and genetic evidence supports the proposal of novel taxa to accommodate these strains; however, because strains HT99 and CC99 cannot be cultured outside of the amoeba host, the respective names 'Candidatus Berkiella aquae' and 'Candidatus Berkiella cookevillensis' are proposed.Free-living amoebae are natural environmental predators of bacteria and other micro-organisms found in soil and water, including anthropogenic systems such as drinking water systems, air conditioners and cooling towers, spas and swimming pools (Rodríguez-Zaragoza, 1994;Benkel et al., 2000;Greub & Raoult, 2004;Berk et al., 2006). Some bacteria only survive engulfment by amoebae whereas other bacteria not only survive but multiply within the amoebal host (Barker & Brown, 1994;Horn & Wagner, 2004;Molmeret et al., 2005). Recent reviews list over 40 genera of bacterial symbionts of amoebae that are human pathogens, making amoebae important environmental reservoirs of virulent bacteria (Lamoth & Greub, 2010;Moliner et al., 2010). Evidence also suggests that amoebae can aid in the selection of virulence traits and the adaptation of bacteria for intracellular survival in human macrophages and other cell types (Cirillo et al., 1994;Greub & Raoult, 2004;Evstigneeva et al., 2009). This report describes two bacterial isolates, HT99 and CC99, that were recovered from amoebae in biofilm samples from constructed aquatic environments (Berk et al., 2006). Both bacteria are amoebaresistant, intranuclear bacteria. We have determined, on the basis of both genotypic and phenotypic characteristics, that these two bacteria do not belong to known genera, justifying the proposal of novel taxa. However, due to the intracellular lifestyle of the bacteria and the lack of pure cultures, we propose the classification of these two bacteria as representatives of 'Candidatus Berkiella aquae' and 'Candidatus Berkiella cookevillensis' and in this report describe the characteristics of both novel bacteria.Bacter...