The complete nucleotide sequences of three sugarcane streak mosaic virus (SCSMV) isolates found in sugarcane plants imported from Japan (JP1, JP2) and Indonesia (ID) into China were determined. Sequence analysis showed that, based on the whole genome sequence and the nucleotide sequences encoding the ten mature proteins, the three SCSMV isolates shared identities of 81.62%-81.67% and 76.39%-85.93%, respectively, with a Pakistan (PAK) isolate of SCSMV. Phylogenetic analysis indicated that SCSMV-JP1, -JP2 and -ID were clustered in a subgroup separate from the previously described SCSMV-PAK and -India isolates, and may thus represent a new strain of SCSMV.