The genetic diversity analysis of 43 agronomic traits was carried out in 45 Zhangpu wild rice germplasms in Fujian Province. The results showed that Zhangpu wild rice represented abundant genetic diversity. 22 of 31 qualitative agronomic traits were found with the variability of genetic differentiation. The genetic diversity indices ranged from 0.245 to 1.43, and the index of leaf color was the highest. The genetic diversity indices of 12 quantitative agronomic traits ranged from 1.86 to 2.06, of which the index of stem length was the highest, indicating that stem length possesses the most abundant genetic diversity. By correlation analysis among 12 quantitative traits, the panicle length represented closely significant positive correlation with the ligule length of flag leaf and the second top leaf, the length and width of flag leaf. 100-grain weight was found to be significant positive correlation with the flowering time and awn length. These materials were clustered into five groups: I, II, III, IV and V, of which the group V was M2042 alone.