Objective To clone and sequence the cDNA encoding farnesyl pyrophosphate synthase(FPS) from Panax notoginseng.Methods The cDNA,encoding FPS in P.notoginseng,was amplified by RACE strategy with the total RNA of root as the template.The fragment of FPS was cloned and sequenced.Results The analysis results revealed that the full-length cDNA had(1 409) bp with an open reading frame encoding 343 amino acids of protein.The FPS sequence had 95%,87%,and 86% amino acid sequence homology to the FPS sequence of Centella asiatica,Parthenium argentatum,and Artemisia annua,respectively. Conclusion The cDNA encoding FPS from P. notoginseng is cloned and reported.This works provide a foundation for exploring the mechanism of saponins biosynthesis and application to the other medical plants.