Abstract:To identify clones of Cryptomeria japonica the Comperation of PCR-RAPD and isozyme anaysis is conducted. With the material of 24 clones from seedling garden-of Fukushima forestry experiment Station in Japan. The results show that isozyme and RAPD with 7 markers cannot identity 24 clones Completely,but RAPD with 17 markers and 27 markers probably identify these 24 clones. The author also consider that isoxyme marker is a genetic marker which exhibits very good reproducibility. So it's fit for genetic structural samility analysis,especially for group genetic analysis,but difficult for individual identifying because the types of isozyme with clear bands is limited. PAPD is a dominant marker which is often unstable,but if Can identify clones corretly with the stable reaction system and condition.