In this study, we used a molecular assay to characterize the biodiversity of the microbial eukaryotic community by analysis of fluid, chimney and sulfide deposits from at the three hydrothermal vent system (i.e. Longqi, Kairei and Edmond), and based on the physical differences between Longqi, Kairei and Edmond, explored how hydrothermal conditions may be important factors for the diversity of the community in these systems.