In this study, we studied the relationship between Hetian rose variety (Rosa rugosa ‘Hetian shamomeigui’) and Zizhi rose (R. rugosa ‘Zizhi’), Fenghua rose (R. rugosa ‘Fenghua’) and Damask rose (R. damascena) with molecular data, investigated the phylogenetic relationship of the Hetian rose within genus Rosa, and discussed its hybridization origin. Results showed that: (1) the Hetian rose had unique genetic source. The genetic distance within the Hetian rose (0.017±0.003) was smaller than the distance between varieties (0.029±0.005, 0.024±0.004, and 0.022±0.003, respectively). (2) The phylogenetic tree showed that GAPDH gene clones of the Hetian rose did not mix with the gene clones from other varieties. These indicated that the Hetian rose was genetically diverged from the other three roses, and should be regarded as an unique rose variety. (3) A part of GAPDH clones of the Hetian rose were clustered with four species (R. bracteata, R. laevigata, R. cymosa, and R. banksiae) in Rosa sect. Bracteatae, sect Laevigatae, and sect. Banksiae from China or Southeast Asia, located at basal position of the phylogenetic tree, while other GAPDH clones were clustered with other four European species (R. elliptica, R. sempervirens, R. trachyphylla, and R. abyssinica) in sects. Caninae, Synstylae, and Gallicanae. A total of 19 GAPDH heterozygous loci were detected between the Hetian rose and the abovementioned closelyrelated species, indicating a hybrid origin of Hetian rose. (4) A close relationship between the Hetian rose and 14 European species from sect. Caninae, sect. Synstylae, and Gallicanae was revealed by cpDNA phylogeny and sequence variation analysis. In conclusion, it was proposed that the Hetian rose had a hybrid origin by Chinese and European rose species or varieties. The hybrid parents may be the one or more species in sects. Bracteatae, Laevigatae, Banksiae, Caninae, Synstylae, and Gallicanae. This study provides a foundation for further research on the probable parental species of the Hetian rose.