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Genetic relationships were estimated among 25 germplasm belonging to Lawsonia inermis L. using RAPD and ISSR markers. These markers were implemented in analyses of principal coordinates (PCO), unweighted pair group mean average (UPGMA). Results showed that the L. inermis L. germplasm divided on three groups based on RAPD data. However, using the ISSR data, all studied germplasm were grouped in one group which is divided on three sub-groups, exception four germplasm. The overall mean genetic similarity based on ISSR data ranged from 0.1 to 0.83 and from 0.07 to 0.83 based on RAPD data. The PCO applied on 25 germplasm using ISSR markers showed three groups constituting the three sub-groups obtained in dendrogram based on UPGMA method.

Based on RAPD data, the PCO and dendrogram defined three groups; only one group seemed to be the same in the two applied analyses. The groups obtained based on ISSR and RAPD were independently from their geographical origin. Therefore the ISSR and RAPD molecular markers show two genetic grouping of L. inermis L. germplasm which would be as the first step to understand and to conserve these resources characterizing by genetic erosion in these localities.