Abstract: 【Objective】To conduct genetic diversity analysis of 63 Baccaurea ramiflora Lour. germplasm resources from Guangxi，Yunnan，Hainan and Guangdong and to establish a preliminary DNA fingerprint，so as to provide a reference for varieties classification，identification，protection，and utilization of B. ramiflora Lour.【Method】Three germplasm resources whose geographical locations were highly different were selected，and the SCoT primers with best quality，repeatability and polymorphism were screened from 75 SCoT primers to perform amplification and electrophoresis on 63 germplasm resources. Genetic diversity and clustering analysis were performed by Popgene 1.32 and NTsys 2.10e and the results were used to construct the fingerprint profiles.【Result】The 6 SCoT primers selected from 63 germplasm resources were used to amplify 192 bands，including 188 polymorphic bands with a polymorphism ratio of 97.86%. The number of bands amplified by each primer ranged from 26 to 36，with an average of 32，and the number of polymorphic bands ranged from 26 to 36，with an average of 31.33 polymorphic bands amplified by each primer，and the polymorphic rate ranged from 90.00% to 100.00%. The polymorphic information content values（PIC）ranged from 0.9052 to 0.9527， with a mean of 0.9319. The Shannon’s information index（I）ranged from 0.2459 to 0.3878，the Nei’s gene diversity（H'） ranged from 0.1476 to 0.2412，the observed number of alleles（Na）ranged from 1.9000 to 2.0000，the number of effective alleles（Ne）ranged from 1.2324 to 1.3700. There were significant differences in polymorphic bands amplified by 6 SCoT primers. The number of germplasms that could be distinguished by single primer was 49-63，with an average of 58. According to the results of cluster analysis，the genetic similarity coefficients（GS）of 63 germplasm resources ranged from 0.5781 to 0.9115，with a mean of 0.7496. At the similarity coefficient of 0.7100，the tested materials were divided into five groups：group A included two germplasm resources from Guangxi；group B included a germplasm resource from Guangxi；group C inclu-ded 4 germplasm resources from Yunnan；group D included all germplasm resources from Hainan and Guangdong；group E included the remaining 50 germplasm resources. 5 SCoT primers（SCoT32，SCoT66， SCoT68，SCoT73，SCoT74）were further screened out to construct the DNA fingerprinting of 63 germplasm resources and each resource had specific DNA fingerprint code in the database.【Conclusion】The 63 germplasm resources are rich in genetic diversity，and there is a certain correlation between the kinship of the germplasm and the geographical area；the six SCoT primers screened are of high polymorphism，which can provide reference for the future studies on evaluation，genetic diversity analysis and fingerprinting on B. ramiflora Lour. germplasm resources.