Background: Human papillomavirus type 16 (HPV16) is the most common etiological cause of cervical cancer in Indonesian women. HPV16 L2 genetic variation analysis is important for vaccine strategies of cervical cancer, yet the data in Indonesia is still limited. In this research, we determined the variation of the HPV16 L2 gene sequences in Indonesian cervical cancer specimens. Method: We cross-sectionally observed a total of 23 DNA isolates of HPV16 positive specimens stored in the laboratory of the Center for Diagnostic and Research on Infectious Diseases (PDRPI Lab) Faculty of Medicine, Universitas Andalas, Padang, Indonesia. The HPV16 L2 genes were amplified, sequenced, and followed by DNA alignment, single nucleotide polymorphisms (SNPs) analysis, and phylogenetic tree reconstruction. Results: As many as 35 SNPs were found, consist of 18 synonymous SNPs (sSNPs) and 17 non-synonymous SNPs (nsSNPs). Amino acid variations were mostly detected at S269P (100%) and L330F (43.48%) with no variation in the immuno-protective region near L2 N-terminus. A total of 5 HPV16 phylogenetic sub-lineages were found closely related to A1 (n=5), A2 (n=12), A3 (n=2), A4 (n=3), and C (n=1). Conclusion: The variation of HPV16 L2 gene sequences was mostly located on the central region of the L2 sequences and the cross-protective region near the L2 N-terminus was particularly conserved. This study should enhance the information about HPV16 L2 gene variation in Indonesia.