Micro-grafted Egyptian grapes were evaluated under in vitro conditions. In vitro Flame seedless cv. scions were grafted on Freedom rootstock shoots. Two methods were used for micro-grafting; alginate matrix and rhizogenic calli. Fluorescein stain was used to sap transport detection through vessels of both scion and rootstock. Biochemical and molecular analyses were used to evaluate successful micro-grafts. Obtained results showed that, In vitro derived shootlets had satisfactory growth. The culture of derived explants formed a successful graft union by alginate matrix (75%) compared to rhizogenic calli (50%) grown shootlets maintained by some roots and leaves formation. There was a significant difference between the two methods in forming a successful graft union and the subsequent growth-related traits. Grafted explants were tested to salinity stress of NaCl: CaCl₂ 1000, 2000 and 3000 ppm. The shoot and root related growth characteristics of the alginate matrix micro grafts were more tolerant to salinity than rhizogenic calli. However, raising salinity level led to growth decrease but alginate plantlets continued forming leaves. RAPD- PCR analysis cleared genetic changes in graft union area reflects a complete scion- rootstock combination, also a hereditary relationship with both was detected and proved micro-grafting success with the two methods. To sum up, micro-grafting is a suitable alternative propagation tool leading to higher growth potential of grafted plants and improving their ability to tolerate different stresses.