Osmanthus fragrans ‘Pucheng Dangui’ is a new ornamental and urban-greening plant variety developed through long-term natural and artificial selection. Urban and rural horticultural industries in Pucheng County, Fujian Province, China, have developed rapidly and many nurseries now grow O. fragrans ‘Pucheng Dangui’ by cuttings. We developed a paternity test and SNP markers for O. fragrans ‘Pucheng Dangui’ using SLAF-seq to identify the fine variety O. fragrans ‘Pucheng Dangui’ based on molecular research. The genome sequence of Fraxinus excelsior was used as the reference to predict restriction enzyme digestion for O. fragrans ‘Pucheng Dangui’. Restriction enzyme digestion fragments between 400 and 480 bp length were defined as SLAF tags digested by the enzyme Hpy166II+EcoRV-HF®. A total of 413,743 SLAF tags was identified, of which 113,061 polymorphic SLAF tags and 353,073 population SNPs were derived. Analysis of the phylogenetic tree, the population admixture structure, the admixture K value cross validation error rate, and the PCA clustering figure showed that all 29 plant samples belonged to the same population, with no significant differences detected between samples. This comprehensive analysis of DNA polymorphisms provided valuable insights into the different individuals or populations of O. fragrans ‘Pucheng Dangui’ and it provided producers and vendors with confidence in the source of their plant material. This results provides a reliable method for researchers to identify O. fragrans ‘Pucheng Dangui’ from other O. fragransspecies or varieties by the molecular approach. The identification of intraspecific genetic variations also provides the basis for further development of individual plant analysis, identification and introgression breeding in other species.