RAPD markers were used to investigate the phylogenetic relationship of section Synstylae in the genus Rosa. A total of 17 Asian taxa, including 14 taxa in section Synstylae, two taxa in section Indicae and R. persica in subgenus Hulthemia, were analyzed with 30 arbitrary primers. From 9 primers, a total of 200 informative DNA fragment bands were obtained, and these bands were then used to calculate their phylogenetic relationship with PAUP. R. luciae and its 4 varieties (R. luciae var. fujisanensis, R. luicae var. onoei, R. luciae var. hakonensis and R. luciae var. paniculigera) formed one clade that is consistent with their similar morphological characters. In this clade, R. luciae and its 2 varieties (R. luciae var. fujisanensis and R. luciae var. onoei) showed a closer relationship, while R. luciae var. hakonensis and R. luciae var. paniculigera are reluctantly separated from them. Another Japanese variety R. multiflora var. adenochaeta was separated from its mother species (R. multiflora). R. multiflora var. adenochaeta has a limited distribution in Kyushu regions of Japan and it has many pink-white flowers clustered in a panicle. In particular, its pedicels and calyx tube are prominently covered with red stipitate glands which is quite different from its mother species. We suppose that R. multiflora var. adenochaeta should be treated as one separate species and be restored to the original name as R. adenochaeta Koidz. Analysis with ITS+matK sequence data also supports our results.