This study classified H5N1 HPAI viruses in Indonesia into three distinct viral lineages (groups 1, 2, and 3) and discovered a group of naturally occurring reassortant viruses that represent a newly emergent H5N1 HPAI strain in Java in 2006. Several phylogenetic methods concurred that two (MP and PB1) of the reassortant viruses' genome segments descended from the group 3 ancestral viruses, and the remaining six (PB2, PA, HA, NP, NA, NS) segments descended from the group 2 ancestral viruses. Although the majority of reassortant viruses (24/25) are human isolates, few of the associated human infections are epidemiologically linked (Table 1) , suggesting multiple sporadic zoonotic transmissions from birds. The phylogeographic results indicate that the parental viruses of the reassortants have been co-circulating in Java since 2005. Despite the identification of parental lineages, the exact number of reassortment events remains difficult to assess. Although the three fairly consistent phylogenetic subgroups (subgroups R1, R2, and R3 in Figure S4 ) formed by the reassortant viruses suggest three independent reassortments, the underlying uncertainty in our estimated phylogenies means that we cannot rule out the possibility of a single origin.