Abstract: Bioinformatic analysis was carried out to predict the functions of S9 segment encoded proteins of Southern rice black streaked dwarf virus (SRBSDV) to provide the scientific basis for further biological function analysis of the encoded proteins of SRBSDV. The S9 segment of SRBSDV Manshi isolate (SRBSDV-YNMShi), which was collected in Manshi, Dehong Prefecture of Yunnan, was amplified by RT-PCR with specific primers. The amplicon was then cloned and sequenced, and the nucleotide sequence of S9 and the amino acid sequences of the encoded proteins were analyzed by bioinformatics. The results showed that, S9 segment of SRBSDV-YNMShi comprises of 1900 nt, and encoded two proteins of P9-1 and P9-2. The nucleotide sequence of S9 segment of SRBSDV-YNMShi shared 99.5%, 99.1%, 98.7% identity with those of Guangdong (GD), Hainan (HN) and Hubei (HB) SRBSDV isolates. Phylogenetic analysis results reconfirmed that SRBSDV was a member of genus Fijivirus, and the isolate of YNMShi could be grouped into the clade of isolates GD and Vietnam other than isolate HN. Bioinformatic analysis results indicated that P9-1 was an unstable hydrophobic protein, and subcellular localized in the nucleus. Random coil was the main structural element of P9-1. Comparison of the amino acid sequences showed that SRBSDV had high homology and similar structure with Rice black streaked dwarf virus (RBSDV) and Maize rough dwarf virus (MRCV). P9-2 was a stabilized hydrophilic protein with two transmembrane domains, and subcellular localized on the plasma membrane.ɑ-helix was the main structural element of P9-2, and a conserved G protein-coupled receptor was detected in the P9-2. P9-1 might be one of the key factors for viral replication, and P2-1 might be a membrane protein with the function of transportation.