Isolates of Newcastle disease virus (NDV) from chicken cases were obtained from various locations in Taiwan during 2003-2006 and were genotypically analyzed by using reverse transcription polymerase chain reaction (RT-PCR) with primers specific to the viral fusion (F) protein gene (534 bp). Part of the amplified F protein DNA product (nucleotide sequence 47-418) and the deduced amino acid sequences were compared phylogenetically with those from strains previously reported in Taiwan and other geographic regions. Our results showed that all Taiwanese isolates (n=20) collected during 2003-2006, according to the phylogenetic tree, belong to the genotype VIId. In addition, all the six Taiwanese isolates obtained in 2003, carry the motif (112)R-R-Q-K-R(116) and have the amino acid L(23) replaced by F(23) (assigned as Group 1). On the other hand, 12 out of the 14 Taiwanese isolates obtained during 2004-2006 possess the motif (112)R-R-K-K-R(116) and have the amino acid G(74), instead of E(74) (assigned as Group 2). To our best knowledge, this is the first reported VIId isolates that possess the sequences of G(74)/(112)R-R-K-K-R(116) within the F0 protein. Since a high mortality, severe clinical signs, typical postmortem lesions, and a high intra-cerebral pathogenicity index (ICPI) were observed in the NDV-infected chickens, these isolates acquired between 2003 and 2006 are considered as the velogenic type. The Group 2 viruses have become dominant and responsible for the majority of Taiwanese outbreaks during recent years. Based on our phylogenetic analysis, it can be postulated that these isolates were evolved from previously reported local strains, and the Group 2 family emerged the latest in the genotype VIId. The information is fundamental to improving the efficiency of controlling strategies and vaccine development for NDV.