Abstract: Minhui3301, an elite restorer line of indica rice, was selected from the hybrids of Minghui86 and Mianhui436 in the pedigree record; but some experimental datas failed to support this genetic relationship. We've found that many morphological traits of Minhui3301 were much more similar to those of R527 than those of Minghui86. In order to find out the genetic origin of Minghui3301, 30 morphological traits and 712 SSR markers of the 4 varieties -Minhui3301, R527, Mianhui436 and Minghui86,were analyzed.Multiple comparisons showed that the morphological traits of Minhui3301 were similar to R527 or Mianhui436, but significantly or very significantly different from Minghui86. Minhui3301, R527 and Mianhui436 were clustered into one group, while Minghui86 was divided into another by cluster analysis at the genetic distance 8.99. Meanwhile, SSR markers analysis showed that the genetic distances between Minhui3301 and R527, Mianhui436,Minghui86 were 0.14, 0.145 and 0.337,respectively. The clustering analysis based on the genetic similarity of molecular markers and morphological traits led to the same conclusion—the SSR band patterns of Minhui3301 were just the combination of R527 and Mianhui436. In short, Minhui3301 was originated from R527 and Mianhui436, but not Minghui86 and Mianhui436.