Eight and seven clones, respectively selected within the olive cultivars `Arbequina' and `Manzanilla de Sevilla', were studied by means of randomly amplified polymorphic DNA (RAPD) and amplified fragment-length polymorphism (AFLP) markers. Two clones of `Arbequina', C3 and C12, showed polymorphism with respect to the standard cultivar by means of both markers. In fact, about 33.6% RAPD bands and 9.2% AFLP bands were polymorphic for these clones. This high level of polymorphism and the presence of a high percentage of bands absent in `Arbequina' suggest their possible origin as `Arbequina' seedlings. The dendrogram obtained by both molecular markers also supports the hypothesis of a seedling origin of these clones as they clustered separately from the original cultivar and the rest of monomorphic clones at low values of similarity. Also within the `Manzanilla de Sevilla' group, two clones (31 and 44) showed diversity with respect to the standard cultivar; 4.5% RAPD and 6.3% AFLP markers were polymorphic for these genotypes while all the other clones didn't show any difference with the standard `Manzanilla de Sevilla'. RAPD and AFLP markers effectively revealed intracultivar variability due to gametic or multiple mutational events, while the detection of other kind of differences such as eventual single mutations remains uncertain and requires further investigation.