Abstract: Genetic polymorphisms of 60 Capsicum annuum L.cultivars were analyzed by using RAPD. Ten from 200 primers were selected for amplification. Seventy DNA fragments and 38 bands showed polymorphisms that occupied 54.3% of the entire amplified bands. Each primer could amplify 4 to 9,averaging 7 bands, polymorphic bands.Most of the amplified fragments had a length ranging from 100 to 2 000 bp. The cluster analysis using DPS software showed that the tested materials could be categorized into 5 groups at D=0.33. The first group included 85 varieties; the second group had only one species, i.e., MLG horn from Shaxian, Fujian; the third group had also only the yellow pepper from Yongan, Fujian; the fourth group contained two cultivars, the small greens hot pepper PBC1752 and PBC81; and the last group, Xiaoxian pepper, PBC932-6-2. All of these speices were genetically closely related with little differentiations among them.