Acanthodactylus is a genus of lacertid lizard, commonly referred to as fringe-fingered lizards or fringe-toed lizards. The systematics of the genus Acanthodactylus was classically based on external morphological traits, osteological characters and morphology of the hemipenes. In this study, partial sequences of 18S rRNA gene were used to estimate the relationships among three lacertide species from Egypt: Acanthodactylus boskianus, Acanthodactylus scutellatus and  Acanthodactylus  longipes. These data were used together with morphological information, to evaluate the relationships among these three species. DNA was extracted from the collected specimens, 988 bp fragment of 18S rRNA was amplified using universal primers and sequenced. The obtained sequences were analyzed and a phylogenetic tree was constructed. Results of analysis revealed that A. scutellatus and A. longipes form a very well supported clade with 86% bootstrap. A. boskianus was found to constitute a separate clade.  The resultant tree based on DNA sequence data was similar to that produced from a differentially weighted data set of morphological characters. In conclusion, the 18S rRNA gene sequence seems to be a good marker for phylogenetic analysis of Acanthodactylus species.