Molecular hydrogen isotope analysis preformed on modern and fossil plants has made a significant impact on diverse research fields in biology and geology. Using living and fossil Metasequoia as an example, we review the technology of online GC-IRMS that made the molecular analysis of hydrogen isotope possible and discuss critical issues concerning with the studies of molecular δD and its applica-tions. The apparent hydrogen fractionation factors between lipid molecules and source water (δwater lipid) vary across plant taxonomy and differ among biomolecules and are affected by multiple environmental factors in which precipitation δD values exercise the first order of control. Eco-physiological factors and environmental parameters are also known to influence δD in plants. Molecular hydrogen isotope analysis of chemically stable lipid molecules, such as n-alkanes, finds a wide range of applications in detecting source sediments, recon-struction of paleoclimatic parameters, inference of air-mass trajectory, as well as in petroleum industry and environmental studies.2009 National Natural Science Foundation of China and Chinese Academy of Sciences. Published by Elsevier Limited and Science in China Press. All rights reserved.