Commercial citrus trees are composed of a scion grafted onto a rootstock. Because grafting is one of the most expensive methods of plant propagation, grafting efficiency is of large practical importance. Recently, Valencia orange trees on root-stocked Volkamer lemon, showed failure grafting. So, they were re-grafted again on a farm located in Um Ammar region of Ismailia governorate. Isolation trials resulted in Alternaria alternate, Fusarium solani and F. equiseti with frequencies i.e. 66.25% 31.37% and 2.11%, respectively from necrotic tissues. Also, the isolation trials were done from all the tested rootstock and scion in the nursery of Horticulture Research Institute (HRI) and the highest frequencies showed with A. alternata on Volkamer lemon (48%) while the lowest frequencies showed with Trifoliate orange (2%). As for Lasiodplodia theobromae, it was isolated only from Volkamer lemon. Also, the isolated fungi were identified using the traditional methods besides molecular bioassay. Pathogenicity experiment was conducted in greenhouse; for the two more frequencies fungi i.e. A. alternate and F. solani, the highest disease incidence percentage was 100% by A. alternate on Navel orange; Valencia scion with Sour orange and Volkamare lemon rootstock. Also, pathogenicity test of the plant samples of HRI nursery was done and the results showed that A. alternata recorded the highest disease incidence (100%) on Navel orange as scion with Sour orange as rootstock. On the opposite it recorded the least disease incidence on Valencia scion with Sour orange rootstock. In an in vitro experiment, the activity of five treatments (H₂O₂, indole acetic acid (IAA), xanthan gum, wood vinegar and control without treatment) was examined against the growth of the pathogenic fungi. IAA (1000 ppm) showed 100% inhibition of both tested fungi mycelial growth. Also in vitro fungicides' activity was estimated on growth inhibition against the two citrus pathogenic fungi mentioned before. Kemazed and Kinol (200 ppm) gave complete inhibition (100%), to F. solani. Also, Kemazed, Kinol, H₂O₂, IAA, and wood vinegar were accomplished in the nursery to assess their efficacy on failure grafting on either scion and rootstock. The wood vinegar and IAA as alternative fungicides gave superior activity against the fungi on the failure grafting percentage compared with the control treatments, whereas they recorded 77.77% reduction in case of A. alternate. Treatments of H₂O₂ gave the highest increase in enzyme activities, while wood vinegar increased the peroxidase, and polyphenol oxidase activities only.