Genetic stability of grafted marula trees within seven lines, some of which exhibiting interline phenotypic variations, was evaluated using the AFLP technique. The study was conducted in two-fold using samples from the DR, LP, MR, OS, PH, SW and TR lines. The genetic analysis using leaf materials indicated varying levels of genetic variations between genotypes within the OS, MR, LP and PH lines. The genotypes of the DR, TR and SW lines showed high intraspecific genetic similarity and formed tight clusters on the UPGMA-based dendrogram. The genetic analysis using a subset of the initial sample set constituting both leaf and barkmaterials which represented the scion and the rootstock components of grafted trees showed high genetic similarities between the graft partners of some genotypes within the OS and PH lines. These high levels of genetic similarity between scion and rootstock partners of a grafted tree suggested that the rootstock graft developed shoots and grew into a tree following graft failure. The observed results imply that grafting is not always successful even within compatible species, however, it can be reliably monitored using molecular markers.