Newcastle disease (ND) is a highly contagious viral disease and has been a constant threat to the poultry industry worldwide. In this study, partial sequences of ND virus (NDV) fusion genome collected from some provinces in Iran during 2010-2012 in vaccinated commercial farms were characterized and compared with other NDV sequences. All viruses showed the amino acid sequence 112 RRQKRF117 at the C-terminus of the F2 protein and phenylalanine at the N-terminus of the F1 protein, residue 117. These amino acid sequences were identical to a known virulent motif. The phylogenetic analysis showed that the Iranian ND isolates in this study are closely related to the genotype VIId of class II NDV strains. The emergence and identification of new sublineages provide an insight into the high rate of genetic drift occurring in NDV strains in Iran, and raise many concerns about the efficacy of current ND control measures in the country.