[Background] Nonpathogenic Epsilonproteobacteria globally distributes in diverse natural environments, especially extreme environments like deep sea hydrothermal vents, are usually detected in microbial communities as a dominant microbial group. Only few hydrothermal Epsilonproteobacteria species have been isolated due to the limitation of current culture technology, which significantly influences our further understanding about their physiological features, metabolic pathways and ecological roles. [Objective] Gaining insight into the phylogenetic position, metabolic potentials and putative roles of uncultured Epsilonproteobacteria in the deep sea hydrothermal communities and vent ecosystems. [Methods] We analyzed the phylogeny and metabolic pathway of four Epsilonproteobacteria reconstructed from the East Pacific Rise deep sea hydrothermal chimney sample based on metagenomic Binning technology. [Results] Bin189 is phylogenetically independent from all other known Epsilonproteobacteria, whereas the other three reconstructed genomes have closed relationship with Nitratiruptor sp. SB155-2. In metabolic potentials, all of reconstructed genomes have the sqr and rTCA carbon fixation pathway related genes, besides they all have the lipopolysaccharide exporter system and multiple secretion system. However, Bin189 has the extra organic matter and amino acid transporters, all of the other three genomes have the complete denitrification pathway and two of them also have the Sox system, hydrogenase as well as the flagella system. [Conclusion] Bin189 very likely is a kind of novel heterotrophic Epsilonproteobacteria detected in the deep sea hydrothermal environments, whereas the other three chemoautotrophic taxa are capable of oxidizing diverse reduced sulfur compounds and hydrogen as energy source. Consequently, these Epsilonproteobacteria are supposed to play crucial roles in the colonization and development of the hydrothermal microbial communities as well as the deep sea geochemical element cycling.