To investigate distributional characteristics of mutations of HPV16 upstream regulatory region (URR) and E6 and E7 oncogene in the patients with cervical cancer in Beijing and to explore the potential association between oncogenesis of cervical cancer and HPV variants in this region, cervical cancer tissue from 31 cases with positive HPV16 were subjected to regular DNA extraction procedure. The corresponding primers were then designed to amplify the target sequence of URR, E6 and E7. The PCR products were sequenced and blast analysis against GenBank was carried out to evaluate the gene mutation and identify the phylogenetic branches. Among all the cases studied, URR was found to be the most frequent mutation fragments, followed by E7, and E6 was the most conservative sequence. A total of 8 hot mutation spot was identi-fied, which were URR G7521A (100%), C7435G (96.77%), C24T (45.16%), A7729C (45.16%), G7839A (45.16%), E6 T178G (41.94%), E7 A647G (45.16%), and T846C (45.16%). The most frequent HPV 16 branch was type As (54.84%), followed by type E (45.16%). Our results suggested that the mutations of G7521A, A7729C, G7839A, T178G, T350G, A647G, and G658A were likely to be associated with the enhanced oncogenic potential of HPV16 and oncogenesis of cer-vical cancer. In Beijing area, two major branches of HPV16 were type As and E. This finding provides valuable information for HPV vaccine development and infection treatment. Type As and E variants had different distributions among various ages and clinic stage groups. It might lead to a new explanation for the getting younger trend of cervical cancer.