Traditionally, phylogenetic interspecies relationships are estimated based on genetic diversity, since it is assumed that the more recently diverged a species, with comparable constancy of development, the more similar their genetic material and proteins should be. However, occasional controversies in the field may reflect limited resolution and accuracy of this approach. Epigenetics has, meanwhile, provided significant evidence that CpG dinucleotides (CpGs) within genetic material are of particular importance for the annotation and function of the genome and the formation of the phenotype, which is continuously shaped by evolutionary interaction with environmental factors. Based on this, it can be concluded that CpGs follow a distinct rate of evolution, compared to all other nucleotide positions. Evidence is provided that supports this conclusion. Therefore, using CpGs to fathom evolutionary relationships between species could turn out to be a valuable approach to achieve, in some cases, an improved understanding of evolutionary development.