The genomic region encompassing the L protein gene and a small open reading frame (ORF 6) of Rice yellow stunt virus (RYSV) has been sequenced, thus completing the nucleotide sequence of the RYSV genome. The genome organization of RYSV is unique in the rhabdoviruses because it contains two additional genes when compared to the basic gene order of the family Rhabdoviridae: Phylogenetic analysis revealed that the amino acid sequence of the RYSV L protein is most closely related to that of the L protein of Sonchus yellows net virus, another nucleorhabdovirus. However, the RYSV L protein has a unique acidic N-terminal domain distinct from that of other rhabdoviruses. Moreover, the polypeptide encoded by the ORF 6 was detected by immunoblot analysis in purified RYSV virions. Thus RYSV provides the first example in the family Rhabdoviridae that a small ORF between the G and L genes encodes a virion protein.