Previous studies have shown that several H5N1 genotypes have emerged in Asia through reassortment between H5N1 viruses and other subtypes [14, 15] . One of these genotypes, Z, predominated the H5N1 outbreaks throughout 2003-2007, causing most H5N1 outbreaks in Asian countries, including Indonesia [16] . Moreover, a variety of antigenically distinct sublineages of Z genotype virus have been established [16] . Unlike Vietnam and Thailand, Indonesia was invaded by only a single sublineage of genotype Z virus. Previous phylogenetic analyses suggested that Hunan province of China may be the source of the initial H5N1 outbreak in Indonesia [17] , and classified the Indonesian H5N1 HPAI viruses into three groups [10] ; however, further statistical analysis is necessary to characterize and compare different aspects of their evolutionary histories. In this study, we examined molecular phylogeny of the most recent Indonesian H5N1 viruses isolated from avian and mammal hosts. A group of putative reassortant viruses was discovered and their genetic parents were identified. In addition, we investigated the evolutionary behaviors (including spatial migration, growth of genetic diversity, and evolutionary drift and selection) of the reassortant viruses and compare with those of the parental strain, thereby providing insights into the nature and impact of this emerging reassortant strain.