Sugarcane yellow leaf virus (SCYLV) is the causal agent of the sugarcane disease Yellow leaf (YL), which was first reported in Hawaii. The presence of SCYLV was detected by tissue blot immunoassay and the Hawaiian sugarcane cultivars fell into susceptible cultivars (with SCYLV) and resistant cultivars (without SCYLV). RT-PCR showed recently that the resistant cultivars also contain the virus, however with a 100-fold lower virus titre than in the susceptible cultivars. SCYLV is present as whole genome (6 kb) or as two subgenomic sequences of 2.4 and 1.0 kb. Virus preparations from three Hawaiian cultivars (one resistant and two susceptible) were fully sequenced and the sequences were aligned to published, full and partial sequences. The phylograms corroborate previous findings that the so-called YLS-segment, which codes for the coat protein, shows the least genetic diversity, whereas the other sequence fragments A–D, representing the ORFs 0–5, expressed a two-fold higher diversity. The Hawaiian SCYLV-strains clustered together next to the Peru strain, apart from the BRA-strains and well apart from the REU-strains. We propose that the Hawaiian SCYLV should be considered as an independent group together with the Peru strain and known as HAW-PER. The sequences from the two susceptible cultivars had a deletion of 48 to 54 nt in ORF1, which codes for the gene silencing suppressor and a RNA-dependent RNA-polymerase. It is speculated that this deletion is important for the high proliferation rate of the virus in the susceptible plants.