Abstract: Objective The nucleoprotein and glycoprotein gene sequences of two rabies virus strains in Taizhou city, Zhejiang province were analyzed to assess the differences between wild strains and the ones used for human and animal rabies vaccines, providing evidence for effective control of rabies. Methods Immunofluorescence assays were performed to analyze 144 dog brain samples collected from Taizhou in 2008. RT-nested PCR was carried out to amplify the entire nucleoprotein and glycoprotein genes of the virus strains. Upon the completion of cloning and sequencing, bioinformatics software was used for analysis of genetic characteristics. Results Two rabies virus strains were isolated from the samples. Sequence analysis showed that both were genotype 1 rabies viruses with 100% homology between their N gene nucleotides and amino acids, and 99.8% and 99.4% between the G gene nucleotides and amino acids, respectively. The isolates held high homologies to CTN vaccine strains in terms of nucleotides: 88.8% for the N genes and between 85.9% and 86.1% for the G genes. With respect to nucleoprotein amino acids, the two demonstrated the highest homology to Hep-Flury vaccine strains, 97.6%, followed by CTN strains, 97.1%. Their homology to CTN glycoprotein amino acids was also high (92.3%-92.5%). Among various rabies virus genotype 1 reference strains, the isolates were most homologous to Zhejiang Wenzhou Wz0(H), Quzhou ZJ-QZ and Indonesian strains. Phylogenetic analysis showed that XY20 and JJ22 were in the closest evolutionary relationship with Zhejiang Wenzhou Wz0 (H), Quzhou ZJ-QZ, Indonesia strains, CTN vaccine strains and Thailand and Malaysia strains, in contrast to a distant one with the vaccine strains, aG, PV and ERA, as well as the standard toxic attacking CVS strains. Conclusion The two rabies viruses isolated from dog brain samples belonged to genotype 1 strains, though both manifested differences from the known genotype 1 and vaccine strains in N and G gene nucleotide sequences, as well as the deduced amino acid sequences.