By the method of PCR product sequencing and cloning sequencing,we sequenced the B and C domains of HBV polymerase gene of the serum samples from 27 hepatitis B surface antigen positive patients and 7 hepatitis B surface antigen negative patients. At the same time, we compared the B and C domains of polymerase gene with that of 8 reported HBV complete sequences. We found that some amino acids are highly conserved. However, there are naturally mutated substitutions in other amino acids. The results showed that the polymerase gene are heterogeneous. It can act as a reference for the research of nucleotide related mutations of polymerase gene.