Ancient biomolecules recovered from fossils and sediments using organic geochemical, biochemical , and molecular biological techniques have provided insight into our understanding of geological and paleobiological events at the molecular level. This paper deals with preservation, recovery and utility of biomolecules in the geological record with emphasis on recent progress of ancient DNA research. Lignin, lipids, carbohydrates, amino acids, and nucleic acids are discussed regarding their structure and recovery techniques. Recent results using DNA sequence data in addressing paleontological questions are also reviewed.