【Objective】 Find a reliable molecular marker to identifyBougainvillea cultivars that are difficult to distinguish, due to cultivar richness and cultivar homonymy and synonymy. 【Method】 A total of 15 simple sequence repeats (SSR) markers were used to amplify DNA samples from 131 Bougainvillea cultivars. SSR amplicons were detected by a capillary electrophoresis method. Cultivar polymorphism and genetic distance were calculated; they were used for clustering analysis and fingerprint construction of all the 131 cultivars.【Result】A total of 85 different alleles were collectively generated by the 15 SSR loci, averaging 5.60 alleles per locus. Shannon’s information index, observed heterozygosity value, and expected heterozygosity value ranged from 0.38 to 1.53, 0.11 to 0.94 and 0.16 to 0.73, with an average of 1.04, 0.50 and 0.57 per locus, respectively. The polymorphism information content ranged from 0.15 to 0.69, with an average of 0.51 per locus. The genetic distance between cultivars ranged from 0.00 to 0.65, with an average of 0.33. Clustering analysis showed that most of the cultivars within a species tended to fall in the same cluster, but some cultivars of the same, whereas certain cultivars from different species were grouped in the same cluster. Several pairs of cultivars were either homonyms or synonyms. Only 11 SSR loci were shown to be effective for identifying the 131 cultivars; thus, the molecular fingerprints of all these cultivars were constructed based on allelic combinations of the 11 markers. 【Conclusion】Further research should be conducted to verify either the Chinese or Latin names of some suspicious cultivars. SSR-based fingerprints ofBougainvillea cultivars constitute a reliable technique for cultivar identification, registration, and intellectual property protection as well as for cultivar clarification in production practices.