Polyacrilamide gel electrophoresis (PAGE) of allozymes was used to investigate the intraspecies genetic variation and the genetic stock structure of Diplodus vulgaris and Lithognathus mormyrus captured from eight localities in the Mediterranean Sea. Twenty-two and 20 putative enzyme-coding loci were examined, respectively, in D. vulgaris and L. mormyrus. Polymorphic loci at the 95% level were used to assess the allozyme variability in D. vulgaris (AAT-2 * , EST-1 * , GLDH * , PEPB-2 * , PGI-2 * , PGM * , SDH * ) and L. mormyrus (AAT-2 * , EST-1 * , GLDH * , MDH-2 * , PGI-2 * , PGM * ). The proportion of polymorphic loci in both species ranged from 0.31 (D. vulgaris) to 0.30 (L. mormyrus), and the observed and expected mean heterozygosity varied between 0.082 and 0.093 (D. vulgaris) and between 0.069 and 0.072 (L. mormyrus). The mean value of observed heterozygosity in D. vulgaris showed a deficit of heterozygosites, thereby indicating a Wahlund effect in the samples examined. Significant genetic differentiation (mean value of θ = 0.013, p < 0.005) was found in D. vulgaris indicating an intraspecific genetic substructure among the samples examined, whereas the mean value of θ = 0.001, p > 0.05 found in L. mormyrus showed a high degree of genetic homogeneity. The results showed the presence of distinct subpopulations of D. vulgaris among the sampled sites, and suggested that analysis of allozymes may provide important information on the genetic stock structure of these two sparids to ensure sustainable management of these species.