This is the crucial report to show direct evidence of deep-sea living benthic archaea by in-situ 13C-tracer experiment. We conducted compound-specific isotope analysis (CSIA) and its intra-molecular isotope analysis for caldarchaeol and crenarchaeol derived from benthic archaea. The CSIA method together with in-situ 13C-tracer experiment can be useful in determining whether sub-seafloor archaea are living or dead. Furthermore, the intra-molecular isotope analysis can be used for the quantitative evaluation of membrane lipid metabolic pathway related to glycerol biosynthesis and isoprenoid biosynthesis.