Human papillomaviruses (HPVs) are a heterogeneous group of small dsDNA viruses which cause a variety of proliferative epithelial lesions at specific anatomical sites. In order to classify HPV protein types, phylogenetic trees were constructed based on amino acid sequence alignments using parsimony and distance matrix algorithms. Simultaneous phylogenetic analysis of E6 and E7 proteins of 42 different HPV strains which mainly found in Homo sapiens was carried out in detail. Both E6 and E7 proteins of different HPV strains showed evolutionary divergence into two major distinct lineages. While E6 protein was further differentiated into 7 smaller lineages, E7 differentiated into 8 lineages. Multiple Sequence Alignment (MSA) results revealed their amino acid profiles demonstrated conserved lineage-specific substitutions independently. The resulting phylogenetic trees provide a classification of the HPVs into specific groups encompassing the known tissue tropism and oncogenic potential of each HPV type. The implications of a phylogenetic taxonomy on the diagnostic detection of HPVs and the concept of different HPV species are discussed. Dendrogram topologies of E6 and E7 proteins among different HPV were very similar which showed that in most of the HPV, both the proteins were evolved in a similar manner. Also, similar phylogenetic profiles among different HPV types having fully / highly conserved residues were observed, suggesting possible functional similarities.