The genetic diversity of 18 soybean cultivars in Fujian were analyzed by RAPD markers. Among 91 RAPD bands obtained from 12 primers, 65 bands were polymorphic which occupied 71.43% of the whole amplified bands. Cluster analysis showed that the tested materials could be divided into three groups at the level of D 0.62, the vegetable soybean materials, the cross-breeding and local varieties and the varieties with semiwild kindred relationship. It also exhibited their relationship related with the geographic origin.