Rice landraces harbour many elite genes modulating important agronomic traits, and are important resources in rice genetic improvement. In this study, 47 pairs of SSR markers and 16 phenotypic traits were deployed to conduct the genetic diversity and clustering analysis of 58 excellent rice landraces. The results showed that 284 polymorphic alleles were amplified from 58 rice landraces with an average of 6.04 alleles (variations: 3 to 10); the polymorphism information content (PIC) ranged from 0.38 to 0.81 with an average of 0.67; and the genetic diversity index (GDI) ranged from 0.76 to 1.88 with an average of 1.36. These suggested that these SSR markers revealed rich polymorphisms and were able to clarity these rice landraces. The variations on 16 phenotypic traits of this collection were largely different; the variation coefficients of awn length, flag leaf angle and filled grains per panicle were 2.15, 0.73 and 0.51, respectively; those of panicle length, growth period, thousand-grain weight and flag leaf width were below 0.2. The clustering analysis showed that the dendrogram of this collection based on either markers or phenotypic traits were generally consistent. In some lines sharing pedigree (Erjiunan 1, Guangluai 4, Lucaihao, Aijiaonant, Jinnante, Guangluai 15), or sister lines (between Hanmadao 1 and Hanmadao 2, Meihuanuo 1 and Meihuanuo 2, Muguanuo 1 and Muguanuo 2, Xiangnuo 1 and Xiangnuo 2), they were clustered together using either of both datasets. Collectively, gained from evaluating the genetic diversity of different rice landraces, this study provided insights in selection of elite parental lines applicable in rice breeding.