Abstract: Wild rice species such as Oryza rufipogon are an important part of Oryza, which are many excellent properties and are a gene bank for rice improvement. This paper proposes that O. rufipogon from Yunnan can be classified into 4 types, namely, Yuanjiang type and purple erect-stem type, green erect-stem type and espalier-growth type from Jinghong. Types were identified by morphologic, such as anther, earring time, and seed shape, and polymorphic analysis with random amplified polymorphic DNA (RAPD) and inter-simple sequence repeats (ISSRs), as well as clustering analysis of markers. A total of 11 ISSR primers and 11 RAPD primers showed polymorphism among the entries. For ISSR markers, 113 polymorphic bands were generated, with 82.26% proportion of polymorphic bands (PPB). For RAPD markers, 76 polymorphic bands were generated, for 76.77% PPB. Gas spectrometry results revealed a significant positive correlation of 0.951 between RAPD and ISSR markers. Clustering analysis by UPGMA showed types of O. rufipogon from Yunnan having significantly different genetic relationships with wild rice species from other areas.