The Clarkia Miocene lacustrine deposit (15-20 Million years old) at the St Maries River Valley in northern Idaho has been a treasure-trove for studying preservation of ancient biomolecules. Previous studies demonstrated that lipid compounds were well preserved in leaf fossils and water-logged sediments, and leaf waxes were still localized inside the leaf tissues after more than 15 million years of burial, providing a unique opportunity to study the preservation of lipid-bound hydrogen isotopes in the deposit. Here, using irm-GC/MS, we demonstrate the preservation of hydrogen isotopic compositions of lipids in Clarkia plant material by measuring D/H in different compounds separated from fractions of Clarkia sediments and fossils. Distinct lipid profiles were obtained from four plant fossils: Metasequoia, Platanus, Quercus, Salix, and sediments. Different D/H values were determined from different lipid compounds derived from the same fossil; the same compound from different fossil genera and sediments yielded distinct dD values. The D/H ratios obtained from ancient lipids fall within the predicted range of modern lipid values derived from living plants. Our reproducible results strongly suggest the preservation of original lipid-bound hydrogen isotopes over 15 million years, indicating that the hydrogen isotope exchange between preserved plant fossils and water was minimal after deposition. The data demonstrate the validity of using hydrogen isotopic compositions of individual lipids for paleoenvironmental and paleoclimatic reconstructions of pre-Quaternary deposition.