Abstract: Background and Objective: Newcastle disease (ND) is an infectious disease caused by ND virus (NDV), which is the major problem in poultry industries. Although vaccination program has been executed in Indonesia, Newcastle disease is still infecting chicken. The lack of vaccine protection against the disease, presumably due to genetic differences between vaccine strain and virus strain in the field. This study was conducted to analyze phylogenetic of Indonesian NDV isolates based on fusion (F) protein-encoding gene, with aim to determine which genotype group of Indonesian NDV isolates, compared to vaccine strain that circulating in Indonesia. Materials and Methods: Samples were RNA genome of NDV, which were isolated from chicken in Kartosuro, Karanganyar; Galur, Kulon Progo and Sukomoro, Magetan areas. The F gene was amplified by one step RT-PCR method and then was sequenced. The genetic variation among samples, other Indonesian isolates, LaSota and B1 vaccine strain were analyzed by pairwise distance method. Phylogenetic tree based on F gene sequence was generated by Neighbor-Joining method (1000 bootstrap repetition) and Kimura-2 parameter model. Result: The genetic variation of F gene nucleotide and F protein amino acid between samples and vaccine strains were higher compared to the variation between samples and other Indonesian isolates. Phylogenetic analysis showed that the samples were included in genotype VII class II, while LaSota and B1 vaccine strain included in genotype II class II. Conclusion: There were differences of fusion protein antigen and genotype group between Indonesian strains and vaccine strains. This finding encouraged to develop ND vaccine based on Indonesian isolates.