In this study, we develop a new three-dimensional (3D) graphical representation technique for protein sequences. Our approach uses the physicochemical properties of 20 amino acids and a BLOSUM62 matrix. This evolutionary information yields perceptive visualizations. For an analysis of protein similarities, a specific vector from 3D graphical representation curves is also formed. Our proposed method is verified on two datasets: first on eight species’ ND6 protein sequences and second on 22 species’ ND5 protein sequences. On the same dataset, the phylogeny achieved by our method agrees with that obtained by other researchers. Our approach, unlike older approaches, does not require the alignment of protein sequences.