Dehalogenating Chloroflexi, such as Dehalococcoidites (Dhc) were originally discovered as the key microorganisms mediating reductive dehalogenation of the prevalent groundwater contaminants tetrachloroethene and trichloroethene. Molecular and genomic studies on their key enzymes for energy conservation, reductive dehalogenases (rdh), have provided evidence for ubiquitous horizontal gene transfer. A pioneering study by Futagami et al. discovered novel putative rdh phylotypes in sediments from the Pacific, revealing an unknown and surprising abundance of rdh genes in pristine habitats. The frequent detection of Dhc-related 16S rRNA genes from these environments implied the occurrence of dissimilatory dehalorespiration in marine subsurface sediments. Despite being ubiquitous in those environments, metabolic life style or ecological function of Dhc in the absence of anthropogenic contaminants is still completely unknown. We therefore analyzed a non-contaminated deep sea sediment sample of the Peru Margin 1230 site by a single cell genomic (SGC) approach. We were able get for the first time data on three single Dhc cells, helping to elucidate their role in the poorly understood oligotrophic marine sub-surface environment. Although all three single cells show the majority of their best Blast hits to Dhc species only one putative reductive dehalogenase was discovered, with very weak similarity to other known sequences. One of the reasons might be the incompleteness of the genome and rdh genes might have been missed. Another possibility is that deep sea Dhc are not halorespirers like their terrestrial relatives. Interestingly, when screening the DNA of other single cells, PCR shows a positive match for a rdh sequence in Firmicutes. This was quite an unexpected twist of the project.