In this study, two markers (RAPD and ISSR) were evaluated for potential use in fingerprinting and determination of the similarity degree between 3 accessions of apple “Douce Djerba” and 8 grafting between Douce Djerba and Anna.

A total of 4 ISSR primers was used and 28 polymorphic alleles were amplified. Four RAPD primers yielded a total of 20 bands, of which 4 (20%) were polymorphic. all accessions were easily distinguishable employing both methods. The similarity coefficient between accessions ranged from 0.692 et 0.923 for ISSR analysis and from 0.875 et 0.933 using the RAPD methodology.

This study indicates that the results obtained based on the RAPD, and ISSR techniques are not significantly correlated. The marker index, based on the effective multiplex ratio and expected heterozygosity, was calculated for both analyses (MI = 2.9 for RAPD and MI = 6.7 for ISSR assays). The ISSR markers were found to be useful for cultivar identification and assessment of phenetic relationships, revealing advantages, due to higher reproducibility, over other RAPD.