The first outbreak of low pathogenic avian influenza (LPAI), H9N2 virus subtype, in 1996 prompted an eradication response, but LPAI returned to Korea in 1999. The relationship between the first and the recurrent viruses is unclear. To determine the molecular epizootiology of recurrent LPAI, we performed phylogenetic analysis with partial nucleotide sequences of four gene segments (HA, NA, NP and PB2) from eight chicken-origin H9N2 viruses. The recurrent H9N2 viruses showed higher nucleotide similarity in haemagglutinin and neuraminidase genes to the 1996 Korean isolates than other Eurasian viruses, and formed a distinct cluster with the early Korean isolates and some isolates from migratory and domestic ducks in Japan and China. Phylogenetic analysis with internal genes showed that some Korean isolates formed a cluster with other subtypes, such as H5N1, H6N1, and H6N2 in China and Taiwan. These results suggest that the recurrent viruses are progeny of the early Korean H9N2 isolates, but further studies are required to explain their phylogenetic relatedness to viruses in China.