Objective : To explore the nucleotide variation and protein amino acid changes of E4 and L2 genes of Human Papillomavirus 16 (HPV16) , and to analyze the evolutionary characteristics of HPV16 virus. Methods : 40 HPV16 infection⁃positive cervical exfoliated cells samples and tissue cell samples were collected from hospital , viral DNA was extracted , Sanger sequencing perform in cervical exfoliated cells DNA and high⁃throughput sequencing technology sequenced in cervical tissues DNA for E4 and L2 genes of HPV16 , HPV16 E4 and L2 gene phylogenetic evolution trees were constructed , and variation of HPV16 E4 and L2 genes were analyzed. Results : There were 72 HPV16 E4 variant samples with nucleotide variants (4 missense mutations and 7 synonymous mutations) at 10 sites , HPV16 L2 gene variants in 74 samples , and nucleotide variants (23 missense mutations and 18 synonymous mutations) at 40 sites. The variation frequency of T4177C , A4288C and A4654C in cervical cancer was significantly higher than that in non⁃cervical cancer, and the difference was statistically significant (P < 0. 05) . Conclusion ① The main HPV16 virus strains in Xinjiang are European strains , and a few are Asian strains. ② The mutation frequency of T4177C , A4288C and A4654C in HPV16 L2 gene is higher than that in non⁃cervical cancer, and G4181A is related to the Asian strain.