Hepatitis B virus infection is highly endemic in China, especially in rural areas such as Dianjiang County with poor-quality health care and little local HBV information. Therefore, for the first time, the present study was carried out to investigate the molecular epidemiology, phylogeny and population dynamics of HBV based on 146 HBV-infected patients. A 435-bp portion of the HBV S region was sequenced, and the phylogeny was reconstructed, indicating that three genotypes, B, C and D of HBV were distributed in Dianjiang County. The predominant genotype is B (67.12 %), followed by C (32.19 %) and D (0.68 %). Patient demographic information and clinical outcomes were examined by genotypes, and no significant association was found. Population dynamics analysis suggested that both genotype B and C have experienced a tenfold expansion during the last five years for reasons that are unclear. Thus, a thorough molecular epidemiology investigation is strongly recommended in the future.