Viral disease investigation in main rice planting areas in Yunnan Province from 2013 to 2014 showed that rice stripe disease, southern rice black-streaked dwarf disease, rice dwarf disease and rice ragged stunt disease were the four major viral diseases threaten rice production in Yunnan Province. Among them, rice stripe disease remained widely distributed in Yunnan with the incidence up to 15.0% in some fields followed by rice dwarf disease occurred in some areas with the highest incidence of 10.0%; and the average incidence of southern rice black-streaked dwarf disease was 5.3%; rice ragged stunt disease occurred with a low incidence. Molecular variation in rice stripe virus (RSV) isolates was analyzed based on the nucleotide sequence of intergenic region (IR) of RNA3 and RNA4. Phylogenetic analysis showed that all of Yunnan RSV isolates could be divided into two distinct clusters. The isolates from Japan, Korea and other provinces of China belonged to groupⅠ, whereas Yunnan isolates fell into both of the two groups and most of them form a distinct Yunnan population of group Ⅱ. The length of IR3 and IR4 varied with RSV isolates,which could be divided into three types of A, B and C according to the difference in the length per 10 nucleotides. Recombination might be occurred during the evolutionary process of RSV since 17 to 21 nucleotides of IR3 and IR4 of some Yunnan isolates shared some identical sequence with their host plants, rice, wheat or barley. We supposed that the high molecular variation of IR3 and IR4 in Yunnan isolates might result from the special geographical and ecological conditions in Yunnan Province.