The Hawaiian Islands are home to a widespread and diverse population of Citrus tristeza virus (CTV), an economically important pathogen of citrus. In this study, we quantified the genetic diversity of two CTV genes and determined the complete genomic sequence for two strains of Hawaiian CTV. The nucleotide diversity was estimated to be 0.0565 + or - 0.0022 for the coat protein (CP) gene (n = 137) and 0.0822 + or - 0.0033 for the p23 gene (n = 30). The genome size and organization of CTV strains HA18-9 and HA16-5 were similar to other fully sequenced strains of CTV. The 3'-terminal halves of their genomes were nearly identical (98.5% nucleotide identity), whereas the 5'-terminal halves were more distantly related (72.3% nucleotide identity), suggesting a possible recombination event. Closer examination of strain HA16-5 indicated that it arose through recent recombination between the movement module of an HA18-9 genotype, and the replication module of an undescribed CTV genotype.