Abstract:Genetic diversity of 12 Freesia refracta accessions was detected and assessed using inter simple sequence repeat (ISSR) markers. From 34 ISSR primers, 12 primers were selected to perform ISSR-PCR. 5~11 DNA fragments were amplified with each of the 12 primers. Total 96 DNA bands were obtained, of which 62 bands had polymorphism, and average 5.2 polymorphic bands per primer. The percentage of polymorphic bands (PPB) was 64.6%. Computed with NTSYS-pc, the genetic distance (GD) of the 12 F. refracta accessions ranged from 0.123 to 0.907, and average 0.442. According to the UPGMA dendrogram based on Nei’s genetic similarity, the 12 materials were divided into 2 groups at 0.56. The accessions with purple flowers belong to the group 1, and the others to the group 2. The results demonstrated that ISSR is a useful tool to analyze the genetic diversity and genetic relationship among F. refracta accessions, which provides a scientific basis for cross breeding and new varieties protection of F. refracta.