The evolutionary phenomena associated with divergence in chemical signals between populations of the same species help to understand the process of speciation. Animals detect and react to semiochemicals and pheromones used in communication. Comparison between populations of the same species that are geographically isolated from one another allows us to determine the genetic or environmental factors responsible for chemical differentiation. Acanthodactylus boskianus from the east and west of Egypt were used as an example to compare the geographical diversity in chemical fingerprints of this species' femoral gland secretions and its phylogeography. Chemical analysis via GC—MS showed that the two geographically distinct populations' odor fingerprints are quantitatively different despite sharing the same components of the secretions. Phylogenetic analysis showed that the eastern and western Egyptian populations are genetically distinct and that chemical divergence of these lizards' odor profiles may be an example of signal evolution.