Abstract: In order to explore the germplasm resource conservation mechanism for the endangered species Cinnamomun micranthum from the molecular level, the most appropriate ISSR-PCR reaction system with its genomic DNA was experimented by optimizing the level of each reacting factors, the primer annealing temperature and cycle parameters. The results showed that the suitable dosage of each reacting factor for C. micranthum ISSR-PCR reaction system was as follows: 20μL reaction system, including 75ng template, 0.4 μmol/L primer, 200 μmol/L dNTP, 1.25 U Taq enzyme, and 1.5 mmol/L Mg2+. The best amplification program was as: denaturation for 7 min at 94 ℃ in advance, then denaturation at 94 ℃ for 30s, annealing for 45s at 530-580 ℃, extension for 90s at 72 ℃, after 45 cycles, extension at 72 ℃ for 7 min, preservation at 4 ℃.