Polyacrylamide gel electrophoreses for malate dehydrogenase (Mdh) and beta-esterase (β-Est) isoenzymes were conducted for biochemical differentiation between two Stenodactylus gekkonid species inhabiting North Sinai of Egypt. Total lipids and proteins of liver and muscle tissues in both species were also analyzed. A total of three Mdh isoforms were recorded in the analysis, in which the activity of Mdh-2 and Mdh-3 seemed to be higher in S. petrii than in S. sthenodactylus. This high activity could be supported by the significant increase in the total lipids and proteins in liver and muscle tissues of the species. It may thus be reasonable to suppose that S. petrii is more active, energetic and adaptable in the desert habitat than S. sthenodactylus. β-Est showed six fractions in S. petrii and only one fraction in S. sthenodactylus. It is therefore noticeable that β-Est is more highly expressed in S. petrii than in S. sthenodactylus.