Genetic diversity of 90 Coix lacryma-jobi germplasm resources collected from the main places of production were analyzed by Sequence-related amplified polymorphism (SRAP) marker, 68 of which were collected from Fujian, 6 from Taiwan, and another 16 from Zhejiang, Liaoning, Shandong, Henan, Yunnan, Jiangsu, Hunan, Guangdong, Shanghai etc. It shows that 26 pairs of primers were selected from 88 pairs of SRAP primers. 26 pairs of SRAP primers produced 185 amplified fragments, of which 157 were polymorphic, accounting for 84.67% of the total. It shows that there is distinct genetic diversity among 90 Coix lacryma-jobi germplasm resources. 90 Coix lacryma-jobi germplasm resources are classified into four categories basing on the UPGMA cluster analysis, which is similar to the result by morphological markers. A DNA fingerprint with 73 Coix lacryma-jobi was constructed by 16 pairs of SRAP primers. There are of significance for genetic research, variety breeding and resource protection of Coix lacryma-jobi.