The lacertid lizard Acanthodactylus scutellatus is common throughout desert areas of Egypt where it inhabits sparsely vegetated sandy desert, but more often vegetated depressions and oases-like situations. A collection of three populations of this lizard from three distinct eco-geographical regions in the Western Desert of Egypt was examined and compared. A numerical cladistic analysis, based on a set of standardized attributes covering pholidosis, as well as morphologic, morphometric characters, was applied to compare the three populations of this species. The analysis identified two morphologically distinct clusters representing two subspecies, one of which is new to science. This new subspecies was fully described; one of the two clusters was found to represent a new distributional record.