A strategy has been developed to screen very rapidly many individuals and loci in one step to screen for qualitative genetic difference among different populations. Genomic DNAs of individuals are digested with a restriction enzyme and then pooled according to the phenotypic character to genetically characterize. After electrophoresis on the same gel of the different DNA pools, the DNA fragments are hybridized with synthetic oligonucleotides of 4 base repeats. The hybridization patterns obtained with the different pools of DNA are compared and are used as references to analyze the individual profiles. This strategy was used to screen the genetic structure of several breeding groups of the European pond turtle (Emys orbicularis) from department of Indre (Brenne region), and Var, both in France at 4 geographic scales. The results are concordant with those obtained using morphological and mtDNA data.